Title: R Interface to Yandex Metrica API
Description: Allows work with 'Management API' for load counters, segments, filters,
user permissions and goals list from Yandex Metrica, 'Reporting API' allows you to get
information about the statistics of site visits and other data without
using the web interface, 'Logs API' allows to receive non-aggregated data and
'Compatible with Google Analytics Core Reporting API v3' allows
receive information about site traffic and other data using field names
from Google Analytics Core API. For more information see official
documents <https://tech.yandex.ru/metrika/doc/api2/concept/about-docpage/>.
Author: Alexey Seleznev <selesnow@gmail.com>
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rym versions 0.5.1 dated 2019-01-17 and 0.5.2 dated 2019-01-23
DESCRIPTION | 8 - MD5 | 34 ++++- R/rym_get_ga.R | 228 ++++++++++++++++++--------------------- R/rym_get_logs.R | 12 +- README.md | 50 +++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/intro-to-rym.Rmd | 92 ++++++--------- inst/doc/intro-to-rym.html | 86 ++++++-------- inst/doc/rym-ga-api.R |only inst/doc/rym-ga-api.Rmd |only inst/doc/rym-ga-api.html |only inst/doc/rym-logs-api.R |only inst/doc/rym-logs-api.Rmd |only inst/doc/rym-logs-api.html |only inst/doc/rym-management-api.R |only inst/doc/rym-management-api.Rmd |only inst/doc/rym-management-api.html |only inst/doc/rym-reporting-api.R |only inst/doc/rym-reporting-api.Rmd |only inst/doc/rym-reporting-api.html |only vignettes/intro-to-rym.Rmd | 92 ++++++--------- vignettes/rym-ga-api.Rmd |only vignettes/rym-logs-api.Rmd |only vignettes/rym-management-api.Rmd |only vignettes/rym-reporting-api.Rmd |only 26 files changed, 297 insertions(+), 305 deletions(-)
Title: R Optimization Infrastructure
Description: The R Optimization Infrastructure ('ROI') is a
sophisticated framework for handling optimization problems in R.
More information can be found on the 'ROI' homepage <http://roi.r-forge.r-project.org/>.
Author: Kurt Hornik [aut],
David Meyer [aut],
Florian Schwendinger [aut],
Stefan Theussl [aut, cre],
Diethelm Wuertz [ctb]
Maintainer: Stefan Theussl <Stefan.Theussl@R-Project.org>
Diff between ROI versions 0.3-1 dated 2018-01-26 and 0.3-2 dated 2019-01-23
ROI-0.3-1/ROI/man/read.op.Rd |only ROI-0.3-1/ROI/man/write.op.Rd |only ROI-0.3-2/ROI/DESCRIPTION | 18 ROI-0.3-2/ROI/MD5 | 66 - ROI-0.3-2/ROI/NAMESPACE | 5 ROI-0.3-2/ROI/R/OP.R | 46 - ROI-0.3-2/ROI/R/bounds.R | 69 + ROI-0.3-2/ROI/R/constraints.R | 2 ROI-0.3-2/ROI/R/io_tools.R | 12 ROI-0.3-2/ROI/R/objective.R | 14 ROI-0.3-2/ROI/R/plugin.R | 8 ROI-0.3-2/ROI/R/reformulations.R | 61 + ROI-0.3-2/ROI/R/roi.R | 37 ROI-0.3-2/ROI/R/utilities.R | 2 ROI-0.3-2/ROI/R/zzz.R | 20 ROI-0.3-2/ROI/man/OP.Rd | 3 ROI-0.3-2/ROI/man/ROI_available_solvers.Rd | 3 ROI-0.3-2/ROI/man/ROI_plugin_add_status_code_to_db.Rd | 4 ROI-0.3-2/ROI/man/ROI_plugin_build_equality_constraints.Rd | 1 ROI-0.3-2/ROI/man/ROI_plugin_build_inequality_constraints.Rd | 4 ROI-0.3-2/ROI/man/ROI_plugin_canonicalize_solution.Rd | 1 ROI-0.3-2/ROI/man/ROI_plugin_get_solver_name.Rd | 1 ROI-0.3-2/ROI/man/ROI_plugin_make_signature.Rd | 1 ROI-0.3-2/ROI/man/ROI_plugin_register_reader_writer.Rd | 7 ROI-0.3-2/ROI/man/ROI_plugin_register_reformulation.Rd | 1 ROI-0.3-2/ROI/man/ROI_plugin_register_solver_control.Rd | 1 ROI-0.3-2/ROI/man/ROI_plugin_register_solver_method.Rd | 6 ROI-0.3-2/ROI/man/ROI_plugin_solution.Rd | 1 ROI-0.3-2/ROI/man/ROI_read.Rd |only ROI-0.3-2/ROI/man/ROI_reformulate.Rd | 1 ROI-0.3-2/ROI/man/ROI_registered_reader.Rd | 4 ROI-0.3-2/ROI/man/ROI_registered_reformulations.Rd | 1 ROI-0.3-2/ROI/man/ROI_registered_solver_control.Rd | 1 ROI-0.3-2/ROI/man/ROI_registered_writer.Rd | 4 ROI-0.3-2/ROI/man/ROI_write.Rd |only ROI-0.3-2/ROI/tests/ROI.R | 416 ----------- 36 files changed, 280 insertions(+), 541 deletions(-)
Title: Project Management Tools
Description: Tools for data importation, recoding, and inspection that
are used at the University of Kansas Center for Research Methods
and Data Analysis. There are functions to create new project
folders, R code templates, create uniquely named output
directories, and to quickly obtain a visual summary for each
variable in a data frame. The main feature here is the systematic
implementation of the "variable key" framework for data
importation and recoding. We are eager to have community feedback
about the variable key and the vignette about it.
Author: Paul Johnson [aut, cre],
Benjamin Kite [aut],
Charles Redmon [aut],
Jared Harpole [ctb],
Kenna Whitley [ctb],
Po-Yi Chen [ctb],
Shadi Pirhosseinloo [ctb]
Maintainer: Paul Johnson <pauljohn@ku.edu>
Diff between kutils versions 1.45 dated 2018-05-19 and 1.60 dated 2019-01-23
DESCRIPTION | 16 ++-- MD5 | 70 +++++++++-------- NAMESPACE | 6 + R/colnamesReplace.R | 19 +++- R/file.backup.R |only R/importQualtrics.R | 145 ++++++++++++++++++++++++++++--------- R/modelcomparison.R | 4 - R/semTable.R | 134 +++++++++++++++++++++------------- R/variableKey.R | 106 ++++++++++++++++++++------- build/vignette.rds |binary data/natlongsurv.RData |binary inst/ChangeLog | 35 ++++++++ inst/doc/variablekey.R | 10 +- inst/doc/variablekey.Rnw | 26 +----- inst/doc/variablekey.pdf |binary inst/unitTests/runit.VariableKey.R | 22 ++++- man/all.equal.keylong.Rd | 3 man/colnamesReplace.Rd | 7 + man/compareLavaan.Rd | 4 - man/deleteBogusRows.Rd | 3 man/file.backup.Rd |only man/importQualtrics.Rd | 34 +++++--- man/initProject.Rd | 4 - man/keyCrossRef.Rd | 3 man/keyImport.Rd | 16 ++-- man/keysPool.Rd | 5 - man/likert.Rd | 4 - man/makeKeylist.Rd | 4 - man/markupConvert.Rd | 26 ++++-- man/mergeCheck.Rd | 4 - man/peek.Rd | 5 - man/print.kutable.Rd |only man/qualtricsBlockStack.Rd |only man/semTable.Rd | 46 ++++++++--- man/starsig.Rd | 3 man/truncsmart.Rd | 4 - man/updatePackages.Rd | 6 - vignettes/variablekey.Rnw | 26 +----- 38 files changed, 529 insertions(+), 271 deletions(-)
Title: A Collection of Statistical Tools for Biologists
Description: Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Author: Ken Aho
Maintainer: Ken Aho <kenaho1@gmail.com>
Diff between asbio versions 1.5-4 dated 2019-01-09 and 1.5-5 dated 2019-01-23
DESCRIPTION | 8 ++++---- MD5 | 42 +++++++++++++++++++++--------------------- R/see.Fcdf.r | 4 ++-- R/see.accPrec.tck.r | 4 ++-- R/see.betacdf.r | 4 ++-- R/see.bincdf.r | 4 ++-- R/see.chicdf.r | 4 ++-- R/see.expcdf.r | 4 ++-- R/see.gamcdf.r | 4 ++-- R/see.geocdf.r | 4 ++-- R/see.hypercdf.r | 4 ++-- R/see.lnormcdf.r | 4 ++-- R/see.logiscdf.r | 4 ++-- R/see.nbincdf.r | 4 ++-- R/see.normcdf.r | 4 ++-- R/see.poiscdf.r | 4 ++-- R/see.smooth.tck.r | 4 ++-- R/see.tcdf.r | 4 ++-- R/see.unifcdf.r | 4 ++-- R/see.weibcdf.r | 4 ++-- inst/doc/ranef.cov.pdf |binary inst/doc/simpson.pdf |binary 22 files changed, 61 insertions(+), 61 deletions(-)
Title: Tools to Handle Taxonomic Lists
Description: Some tools to work with taxonomic name lists.
Author: Vijay Barve [aut, cre] (<https://orcid.org/0000-0002-4852-2567>)
Maintainer: Vijay Barve <vijay.barve@gmail.com>
Diff between taxotools versions 0.0.4 dated 2018-09-28 and 0.0.5 dated 2019-01-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 3 ++- R/ExpandSyn.R | 7 ++++++- README.md | 3 +++ man/ExpandSyn.Rd | 3 ++- 6 files changed, 22 insertions(+), 12 deletions(-)
Title: R6 Objects for Text and Data
Description: For natural language processing and analysis of qualitative text
coding structures which provide a way to bind together text and text data
are fundamental. The package provides such a structure and accompanying
methods in form of R6 objects. The 'rtext' class allows for text handling
and text coding (character or regex based) including data updates on
text transformations as well as aggregation on various levels.
Furthermore, the usage of R6 enables inheritance and passing by reference
which should enable 'rtext' instances to be used as back-end for R based
graphical text editors or text coding GUIs.
Author: Peter Meissner [aut, cre],
Ulrich Sieberer [cph],
University of Konstanz [cph]
Maintainer: Peter Meissner <retep.meissner@gmail.com>
Diff between rtext versions 0.1.20 dated 2016-11-01 and 0.1.21 dated 2019-01-23
rtext-0.1.20/rtext/tests/testthat/NA |only rtext-0.1.21/rtext/DESCRIPTION | 10 rtext-0.1.21/rtext/MD5 | 83 +++--- rtext-0.1.21/rtext/NAMESPACE | 36 +- rtext-0.1.21/rtext/NEWS.md | 15 + rtext-0.1.21/rtext/R/RcppExports.R | 30 +- rtext-0.1.21/rtext/R/rtext_loadsave.R | 5 rtext-0.1.21/rtext/README.md | 157 ++++++++--- rtext-0.1.21/rtext/inst/CITATION | 2 rtext-0.1.21/rtext/man/R6_rtext_extended.Rd | 41 +-- rtext-0.1.21/rtext/man/bind_between.Rd | 39 +- rtext-0.1.21/rtext/man/classes.Rd | 31 +- rtext-0.1.21/rtext/man/dim1.Rd | 31 +- rtext-0.1.21/rtext/man/dim2.Rd | 31 +- rtext-0.1.21/rtext/man/dp_arrange.Rd | 35 +- rtext-0.1.21/rtext/man/get_vector_element.Rd | 43 +-- rtext-0.1.21/rtext/man/is_between.Rd | 39 +- rtext-0.1.21/rtext/man/load_into.Rd | 31 +- rtext-0.1.21/rtext/man/modus.Rd | 37 +- rtext-0.1.21/rtext/man/pipe.Rd | 19 - rtext-0.1.21/rtext/man/plot.rtext.Rd | 51 +-- rtext-0.1.21/rtext/man/prometheus_early.Rd | 35 +- rtext-0.1.21/rtext/man/prometheus_late.Rd | 35 +- rtext-0.1.21/rtext/man/rbind_fill.Rd | 35 +- rtext-0.1.21/rtext/man/read_utf8_csv.Rd | 35 +- rtext-0.1.21/rtext/man/rtext.Rd | 210 ++++++++-------- rtext-0.1.21/rtext/man/rtext_base.Rd | 41 +-- rtext-0.1.21/rtext/man/rtext_export.Rd | 41 +-- rtext-0.1.21/rtext/man/rtext_get_character.Rd | 43 +-- rtext-0.1.21/rtext/man/rtext_hash.Rd | 31 +- rtext-0.1.21/rtext/man/rtext_loadsave.Rd | 41 +-- rtext-0.1.21/rtext/man/rtext_tokenize.Rd | 41 +-- rtext-0.1.21/rtext/man/seq_dim1.Rd | 31 +- rtext-0.1.21/rtext/man/shift.Rd | 51 +-- rtext-0.1.21/rtext/man/testfile.Rd | 35 +- rtext-0.1.21/rtext/man/text_tokenize.rtext.Rd | 66 ++--- rtext-0.1.21/rtext/man/vector_delete.Rd | 43 +-- rtext-0.1.21/rtext/man/which_token.Rd | 39 +- rtext-0.1.21/rtext/man/which_token_worker.Rd | 51 +-- rtext-0.1.21/rtext/man/write_utf8_csv.Rd | 35 +- rtext-0.1.21/rtext/src/RcppExports.cpp | 12 rtext-0.1.21/rtext/tests/testthat/test_rtext_loadsave.R | 9 rtext-0.1.21/rtext/tests/testthat/test_tools.R | 20 + 43 files changed, 917 insertions(+), 829 deletions(-)
Title: Rothman's Episheet
Description: A collection of R functions supporting the text book
Modern Epidemiology, Second Edition, by Kenneth J.Rothman and Sander Greenland.
ISBN 13: 978-0781755641 See <http://www.krothman.org/> for more information.
Author: James Black [aut, cre],
Ken Rothman [cph],
Simon Thelwall [ctb] (<https://orcid.org/0000-0002-0434-2724>)
Maintainer: James Black <james@epijim.uk>
Diff between episheet versions 0.3.0 dated 2018-10-22 and 0.4.0 dated 2019-01-23
DESCRIPTION | 8 ++++---- MD5 | 21 +++++++++++++-------- NAMESPACE | 1 + NEWS.md | 8 ++++++++ R/data.R | 21 +++++++++++++++++++++ R/rate.R |only R/risk.R | 9 +++++---- R/stratified_risk.R | 4 ++-- data/ebola.rda |only inst/doc/pvalueplot.html | 38 +++++++++++++++++++++++++++++--------- man/ebola.Rd |only man/rate.Rd |only tests/testthat/test-rate.R |only tests/testthat/test-risk.R | 24 +++++++++++++++--------- 14 files changed, 98 insertions(+), 36 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-05-12 1.0.4
2017-04-18 1.0.3
2015-06-22 1.0.2
2014-10-09 1.0.1
2014-09-01 0.1.1
2014-05-21 0.1.0
2014-04-13 0.0.1
Title: Simulate Models Based on the Generalized Linear Model
Description: Easily simulates regression models,
including both simple regression and generalized linear mixed
models with up to three level of nesting. Power simulations that are
flexible allowing the specification of missing data, unbalanced designs,
and different random error distributions are built into the package.
Author: Brandon LeBeau [aut, cre]
Maintainer: Brandon LeBeau <lebebr01+simglm@gmail.com>
Diff between simglm versions 0.7.1 dated 2018-07-25 and 0.7.2 dated 2019-01-23
DESCRIPTION | 8 MD5 | 152 NAMESPACE | 164 NEWS.md | 3 R/missing_data.r | 2 R/pow_sim.r | 17 README.md | 137 build/vignette.rds |binary inst/doc/GeneralizedModels_legacy.R | 152 inst/doc/GeneralizedModels_legacy.html | 854 +- inst/doc/Intro_legacy.R | 378 - inst/doc/Intro_legacy.html | 1314 +-- inst/doc/Power_legacy.R | 474 - inst/doc/Power_legacy.html | 1238 +-- inst/doc/simulation_arguments.R | 888 +- inst/doc/simulation_arguments.html |12310 ++++++++++++++++----------------- inst/doc/tidy_simulation.R | 518 - inst/doc/tidy_simulation.html | 1748 ++-- inst/doc/unbalanced_legacy.R | 332 inst/doc/unbalanced_legacy.html | 1422 +-- man/compute_statistics.Rd | 66 man/corr_variables.Rd | 48 man/cross_class.Rd | 68 man/data_glm_nested.Rd | 60 man/data_glm_nested3.Rd | 74 man/data_glm_single.Rd | 48 man/data_reg_nested.Rd | 54 man/data_reg_nested3.Rd | 67 man/data_reg_single.Rd | 50 man/desireVar.Rd | 68 man/extract_coefficients.Rd | 34 man/generate_missing.Rd | 44 man/generate_response.Rd | 56 man/missing.Rd | 113 man/model_fit.Rd | 52 man/parse_crossclass.Rd | 34 man/parse_formula.Rd | 40 man/parse_power.Rd | 40 man/parse_randomeffect.Rd | 28 man/parse_varyarguments.Rd | 40 man/rbimod.Rd | 86 man/replicate_simulation.Rd | 59 man/run_shiny.Rd | 32 man/sim_continuous.Rd | 56 man/sim_continuous2.Rd | 68 man/sim_err_nested.Rd | 114 man/sim_err_single.Rd | 116 man/sim_factor.Rd | 56 man/sim_factor2.Rd | 54 man/sim_fixef_nested.Rd | 142 man/sim_fixef_nested3.Rd | 142 man/sim_fixef_single.Rd | 124 man/sim_glm.Rd | 435 - man/sim_glm_nested.Rd | 290 man/sim_glm_nested3.Rd | 351 man/sim_glm_single.Rd | 182 man/sim_knot.Rd | 58 man/sim_pow.Rd | 624 - man/sim_pow_glm.Rd | 454 - man/sim_pow_glm_nested.Rd | 337 man/sim_pow_glm_nested3.Rd | 375 - man/sim_pow_glm_single.Rd | 228 man/sim_pow_nested.Rd | 381 - man/sim_pow_nested3.Rd | 424 - man/sim_pow_single.Rd | 263 man/sim_rand_eff.Rd | 80 man/sim_reg.Rd | 495 - man/sim_reg_nested.Rd | 347 man/sim_reg_nested3.Rd | 397 - man/sim_reg_single.Rd | 236 man/sim_time.Rd | 38 man/simglm.Rd | 63 man/simulate_error.Rd | 48 man/simulate_fixed.Rd | 50 man/simulate_randomeffect.Rd | 50 man/transform_outcome.Rd | 36 man/varcov_randeff.Rd | 36 77 files changed, 15333 insertions(+), 15189 deletions(-)
Title: Paired Response Curve
Description: Estimation, prediction and testing for analyzing serial dilution assay data (Fong and Yu 2015 <DOI:10.1080/19466315.2015.1093019>) using paired response curve, which is a model of the nonlinear functional relationship between experimental outcomes measured at two different dilutions.
Author: Youyi Fong
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between prc versions 2018.8-17 dated 2018-08-17 and 2019.1-23 dated 2019-01-23
ChangeLog | 5 ++++- DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/unitTests/runit.prcsp.R | 19 ++++++++++--------- 4 files changed, 20 insertions(+), 16 deletions(-)
Title: Tools for Analyzing MCMC Simulations from Bayesian Inference
Description: Tools for assessing and diagnosing convergence of
Markov Chain Monte Carlo simulations, as well as for graphically display
results from full MCMC analysis. The package also facilitates the graphical
interpretation of models by providing flexible functions to plot the
results against observed variables.
Author: Xavier Fernández i Marín <xavier.fim@gmail.com>
Maintainer: ORPHANED
Diff between ggmcmc versions 1.1 dated 2016-06-28 and 1.1.1 dated 2019-01-23
DESCRIPTION | 12 MD5 | 18 - build/vignette.rds |binary inst/doc/using_ggmcmc.Rmd | 2 inst/doc/using_ggmcmc.html | 560 +++++++++++++++++++++++++++++++-------------- inst/doc/v70i09.R | 8 inst/doc/v70i09.Rnw | 2 inst/doc/v70i09.pdf |binary vignettes/using_ggmcmc.Rmd | 2 vignettes/v70i09.Rnw | 2 10 files changed, 420 insertions(+), 186 deletions(-)
Title: Simulate from ODE-Based Models
Description: Fast simulation from ordinary differential equation (ODE) based
models typically employed in quantitative pharmacology and systems biology.
Author: Kyle T Baron [aut, cre] (<https://orcid.org/0000-0001-7252-5656>),
Alan C Hindmarsh [ctb],
Linda R Petzold [ctb],
Bill Gillespie [ctb],
Charles Margossian [ctb],
Devin Pastoor [ctb],
Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>),
Metrum Research Group [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>
Diff between mrgsolve versions 0.8.12 dated 2018-04-27 and 0.9.0 dated 2019-01-23
mrgsolve-0.8.12/mrgsolve/R/class_modlist.R |only mrgsolve-0.8.12/mrgsolve/R/mcache.R |only mrgsolve-0.8.12/mrgsolve/inst/include/modelheader.h |only mrgsolve-0.8.12/mrgsolve/inst/include/mrgsolv.h |only mrgsolve-0.8.12/mrgsolve/inst/models/firstmodel.cpp |only mrgsolve-0.8.12/mrgsolve/inst/models/firstmodelExample.cpp |only mrgsolve-0.8.12/mrgsolve/inst/models/pkpdExample.cpp |only mrgsolve-0.8.12/mrgsolve/inst/models/popExample.cpp |only mrgsolve-0.8.12/mrgsolve/inst/models/viralExample.cpp |only mrgsolve-0.8.12/mrgsolve/inst/project/housemodel.RDS |only mrgsolve-0.8.12/mrgsolve/man/as.list_mrgmod.Rd |only mrgsolve-0.8.12/mrgsolve/man/as_bmat.Rd |only mrgsolve-0.8.12/mrgsolve/man/bmat.Rd |only mrgsolve-0.8.12/mrgsolve/man/chain.Rd |only mrgsolve-0.8.12/mrgsolve/man/do_mrgsim.Rd |only mrgsolve-0.8.12/mrgsolve/man/events.Rd |only mrgsolve-0.8.12/mrgsolve/man/modlist-class.Rd |only mrgsolve-0.8.12/mrgsolve/man/modlist.Rd |only mrgsolve-0.8.12/mrgsolve/man/relocate.Rd |only mrgsolve-0.8.12/mrgsolve/man/rename_cols.Rd |only mrgsolve-0.8.12/mrgsolve/man/show-modlist-method.Rd |only mrgsolve-0.8.12/mrgsolve/man/valid_data.Rd |only mrgsolve-0.8.12/mrgsolve/src/quick.cpp |only mrgsolve-0.9.0/mrgsolve/DESCRIPTION | 67 - mrgsolve-0.9.0/mrgsolve/MD5 | 421 +++++----- mrgsolve-0.9.0/mrgsolve/NAMESPACE | 44 - mrgsolve-0.9.0/mrgsolve/R/Aaaa.R | 24 mrgsolve-0.9.0/mrgsolve/R/RcppExports.R | 12 mrgsolve-0.9.0/mrgsolve/R/annot.R | 44 - mrgsolve-0.9.0/mrgsolve/R/chain.R | 47 - mrgsolve-0.9.0/mrgsolve/R/class_build.R | 147 +++ mrgsolve-0.9.0/mrgsolve/R/class_derived.R | 16 mrgsolve-0.9.0/mrgsolve/R/class_ev.R | 45 - mrgsolve-0.9.0/mrgsolve/R/class_matlist.R | 38 mrgsolve-0.9.0/mrgsolve/R/class_mrgmod.R | 217 +++-- mrgsolve-0.9.0/mrgsolve/R/class_mrgsims.R | 9 mrgsolve-0.9.0/mrgsolve/R/class_numericlist.R | 17 mrgsolve-0.9.0/mrgsolve/R/class_rx.R |only mrgsolve-0.9.0/mrgsolve/R/class_tgrid.R | 9 mrgsolve-0.9.0/mrgsolve/R/compile.R | 23 mrgsolve-0.9.0/mrgsolve/R/data_set.R | 80 + mrgsolve-0.9.0/mrgsolve/R/datasets.R | 4 mrgsolve-0.9.0/mrgsolve/R/env.R | 5 mrgsolve-0.9.0/mrgsolve/R/events.R | 177 ++-- mrgsolve-0.9.0/mrgsolve/R/funset.R | 38 mrgsolve-0.9.0/mrgsolve/R/generics.R | 40 mrgsolve-0.9.0/mrgsolve/R/idata_set.R | 31 mrgsolve-0.9.0/mrgsolve/R/init.R | 39 mrgsolve-0.9.0/mrgsolve/R/inven.R | 17 mrgsolve-0.9.0/mrgsolve/R/knobs.R | 43 - mrgsolve-0.9.0/mrgsolve/R/matlist.R | 47 - mrgsolve-0.9.0/mrgsolve/R/matrix.R | 106 +- mrgsolve-0.9.0/mrgsolve/R/mcode.R | 17 mrgsolve-0.9.0/mrgsolve/R/model_include.R | 38 mrgsolve-0.9.0/mrgsolve/R/modlib.R | 32 mrgsolve-0.9.0/mrgsolve/R/modspec.R | 235 ++++- mrgsolve-0.9.0/mrgsolve/R/mread.R | 239 ++--- mrgsolve-0.9.0/mrgsolve/R/mrgindata.R | 207 +++- mrgsolve-0.9.0/mrgsolve/R/mrgsim_q.R |only mrgsolve-0.9.0/mrgsolve/R/mrgsims.R | 108 +- mrgsolve-0.9.0/mrgsolve/R/mrgsolve.R | 337 ++++---- mrgsolve-0.9.0/mrgsolve/R/nmxml.R | 83 + mrgsolve-0.9.0/mrgsolve/R/package.R | 45 - mrgsolve-0.9.0/mrgsolve/R/param.R | 58 - mrgsolve-0.9.0/mrgsolve/R/print.R | 203 ++-- mrgsolve-0.9.0/mrgsolve/R/qsim.R | 226 ----- mrgsolve-0.9.0/mrgsolve/R/realize_addl.R | 28 mrgsolve-0.9.0/mrgsolve/R/relabel.R | 2 mrgsolve-0.9.0/mrgsolve/R/render.R | 12 mrgsolve-0.9.0/mrgsolve/R/update.R | 36 mrgsolve-0.9.0/mrgsolve/R/utils.R | 104 +- mrgsolve-0.9.0/mrgsolve/R/workflows.R |only mrgsolve-0.9.0/mrgsolve/inst/Rmd/mrgsolve_render_template.Rmd | 8 mrgsolve-0.9.0/mrgsolve/inst/WORDLIST |only mrgsolve-0.9.0/mrgsolve/inst/base/databox_cpp.h |only mrgsolve-0.9.0/mrgsolve/inst/base/modelheader.h | 46 - mrgsolve-0.9.0/mrgsolve/inst/base/mrgsolv.h | 82 + mrgsolve-0.9.0/mrgsolve/inst/include/dataobject.h | 12 mrgsolve-0.9.0/mrgsolve/inst/include/datarecord.h | 4 mrgsolve-0.9.0/mrgsolve/inst/include/mrgsolve.h | 18 mrgsolve-0.9.0/mrgsolve/inst/include/odepack_dlsoda.h | 2 mrgsolve-0.9.0/mrgsolve/inst/include/odeproblem.h | 80 - mrgsolve-0.9.0/mrgsolve/inst/models/MODLIST | 5 mrgsolve-0.9.0/mrgsolve/inst/models/emax.cpp | 15 mrgsolve-0.9.0/mrgsolve/inst/models/irm1.cpp | 14 mrgsolve-0.9.0/mrgsolve/inst/models/pbpk.cpp |only mrgsolve-0.9.0/mrgsolve/inst/models/pk2iv.cpp |only mrgsolve-0.9.0/mrgsolve/inst/models/pred1.cpp |only mrgsolve-0.9.0/mrgsolve/inst/mrgx/mrgx.h | 2 mrgsolve-0.9.0/mrgsolve/inst/mrgx/simeta.h | 2 mrgsolve-0.9.0/mrgsolve/inst/msg |only mrgsolve-0.9.0/mrgsolve/inst/project/housemodel.cpp | 2 mrgsolve-0.9.0/mrgsolve/man/BLOCK_PARSE.Rd | 5 mrgsolve-0.9.0/mrgsolve/man/PKMODEL.Rd | 22 mrgsolve-0.9.0/mrgsolve/man/Req.Rd | 3 mrgsolve-0.9.0/mrgsolve/man/as.ev.Rd | 6 mrgsolve-0.9.0/mrgsolve/man/as.list-mrgmod-method.Rd |only mrgsolve-0.9.0/mrgsolve/man/as.list-mrgsims-method.Rd | 4 mrgsolve-0.9.0/mrgsolve/man/as_data_set.Rd | 4 mrgsolve-0.9.0/mrgsolve/man/as_deslist.Rd | 2 mrgsolve-0.9.0/mrgsolve/man/cama.Rd | 1 mrgsolve-0.9.0/mrgsolve/man/cmt_list-class.Rd | 4 mrgsolve-0.9.0/mrgsolve/man/cvec.Rd | 2 mrgsolve-0.9.0/mrgsolve/man/data_qsim.Rd | 17 mrgsolve-0.9.0/mrgsolve/man/data_set.Rd | 34 mrgsolve-0.9.0/mrgsolve/man/design.Rd | 1 mrgsolve-0.9.0/mrgsolve/man/details.Rd | 22 mrgsolve-0.9.0/mrgsolve/man/env_get.Rd | 2 mrgsolve-0.9.0/mrgsolve/man/ev-class.Rd | 1 mrgsolve-0.9.0/mrgsolve/man/ev.Rd | 44 - mrgsolve-0.9.0/mrgsolve/man/ev_days.Rd | 4 mrgsolve-0.9.0/mrgsolve/man/ev_methods.Rd | 26 mrgsolve-0.9.0/mrgsolve/man/ev_ops.Rd | 1 mrgsolve-0.9.0/mrgsolve/man/ev_rx.Rd |only mrgsolve-0.9.0/mrgsolve/man/ev_seq.Rd | 2 mrgsolve-0.9.0/mrgsolve/man/exdatasets.Rd | 4 mrgsolve-0.9.0/mrgsolve/man/expand.idata.Rd | 18 mrgsolve-0.9.0/mrgsolve/man/expand_observations.Rd |only mrgsolve-0.9.0/mrgsolve/man/file_show.Rd | 5 mrgsolve-0.9.0/mrgsolve/man/house.Rd | 2 mrgsolve-0.9.0/mrgsolve/man/idata_set.Rd | 29 mrgsolve-0.9.0/mrgsolve/man/init.Rd | 27 mrgsolve-0.9.0/mrgsolve/man/is.mrgsims.Rd | 4 mrgsolve-0.9.0/mrgsolve/man/knobs.Rd | 20 mrgsolve-0.9.0/mrgsolve/man/loadso.Rd | 32 mrgsolve-0.9.0/mrgsolve/man/lower2matrix.Rd | 1 mrgsolve-0.9.0/mrgsolve/man/matlist-class.Rd | 1 mrgsolve-0.9.0/mrgsolve/man/matlist.Rd | 24 mrgsolve-0.9.0/mrgsolve/man/matlist_ops.Rd | 4 mrgsolve-0.9.0/mrgsolve/man/matrix_converters.Rd |only mrgsolve-0.9.0/mrgsolve/man/matrix_helpers.Rd |only mrgsolve-0.9.0/mrgsolve/man/mcode.Rd | 13 mrgsolve-0.9.0/mrgsolve/man/merge.Rd | 1 mrgsolve-0.9.0/mrgsolve/man/mod.Rd | 1 mrgsolve-0.9.0/mrgsolve/man/modMATRIX.Rd | 1 mrgsolve-0.9.0/mrgsolve/man/modelparse.Rd | 17 mrgsolve-0.9.0/mrgsolve/man/modlib.Rd | 15 mrgsolve-0.9.0/mrgsolve/man/modlib_details.Rd | 2 mrgsolve-0.9.0/mrgsolve/man/modlib_pkpd.Rd | 2 mrgsolve-0.9.0/mrgsolve/man/modlib_tmdd.Rd | 2 mrgsolve-0.9.0/mrgsolve/man/mread.Rd | 57 - mrgsolve-0.9.0/mrgsolve/man/mrgmod-class.Rd | 25 mrgsolve-0.9.0/mrgsolve/man/mrgmod_extract.Rd |only mrgsolve-0.9.0/mrgsolve/man/mrgsim.Rd | 164 ++- mrgsolve-0.9.0/mrgsolve/man/mrgsim_q.Rd |only mrgsolve-0.9.0/mrgsolve/man/mrgsim_variants.Rd | 16 mrgsolve-0.9.0/mrgsolve/man/mrgsims-class.Rd | 5 mrgsolve-0.9.0/mrgsolve/man/mrgsims.Rd | 20 mrgsolve-0.9.0/mrgsolve/man/mrgsims_dplyr.Rd | 5 mrgsolve-0.9.0/mrgsolve/man/mrgsolve_package.Rd | 33 mrgsolve-0.9.0/mrgsolve/man/mvgauss.Rd | 1 mrgsolve-0.9.0/mrgsolve/man/nmxml.Rd | 6 mrgsolve-0.9.0/mrgsolve/man/numeric2diag.Rd | 1 mrgsolve-0.9.0/mrgsolve/man/numericlist-class.Rd | 1 mrgsolve-0.9.0/mrgsolve/man/numericlist.Rd | 12 mrgsolve-0.9.0/mrgsolve/man/numerics_only.Rd |only mrgsolve-0.9.0/mrgsolve/man/param.Rd | 45 - mrgsolve-0.9.0/mrgsolve/man/parameter_list-class.Rd | 4 mrgsolve-0.9.0/mrgsolve/man/plot_batch_mrgsims.Rd | 8 mrgsolve-0.9.0/mrgsolve/man/plot_mrgsims.Rd | 9 mrgsolve-0.9.0/mrgsolve/man/qsim.Rd | 28 mrgsolve-0.9.0/mrgsolve/man/read_nmext.Rd | 13 mrgsolve-0.9.0/mrgsolve/man/recmatrix.Rd | 3 mrgsolve-0.9.0/mrgsolve/man/render.Rd | 6 mrgsolve-0.9.0/mrgsolve/man/reserved.Rd | 4 mrgsolve-0.9.0/mrgsolve/man/scrape_and_call.Rd | 7 mrgsolve-0.9.0/mrgsolve/man/scrape_opts.Rd | 16 mrgsolve-0.9.0/mrgsolve/man/show-cmt_list-method.Rd |only mrgsolve-0.9.0/mrgsolve/man/show-mrgmod-method.Rd | 1 mrgsolve-0.9.0/mrgsolve/man/show-parameter_list-method.Rd |only mrgsolve-0.9.0/mrgsolve/man/sigma.Rd | 3 mrgsolve-0.9.0/mrgsolve/man/simargs.Rd | 8 mrgsolve-0.9.0/mrgsolve/man/solversettings.Rd | 4 mrgsolve-0.9.0/mrgsolve/man/stime.Rd | 1 mrgsolve-0.9.0/mrgsolve/man/tgrid.Rd | 5 mrgsolve-0.9.0/mrgsolve/man/touch_funs.Rd | 3 mrgsolve-0.9.0/mrgsolve/man/tscale.Rd | 4 mrgsolve-0.9.0/mrgsolve/man/valid_data_set.Rd |only mrgsolve-0.9.0/mrgsolve/man/valid_idata_set.Rd |only mrgsolve-0.9.0/mrgsolve/man/wf_sweep.Rd |only mrgsolve-0.9.0/mrgsolve/man/zchain.Rd | 8 mrgsolve-0.9.0/mrgsolve/src/Makevars | 10 mrgsolve-0.9.0/mrgsolve/src/Makevars.win | 7 mrgsolve-0.9.0/mrgsolve/src/RcppExports.cpp | 55 - mrgsolve-0.9.0/mrgsolve/src/dataobject.cpp | 100 +- mrgsolve-0.9.0/mrgsolve/src/datarecord.cpp | 27 mrgsolve-0.9.0/mrgsolve/src/devtran.cpp | 171 +++- mrgsolve-0.9.0/mrgsolve/src/housemodel-mread-source.cpp | 37 mrgsolve-0.9.0/mrgsolve/src/mrgsimq.cpp |only mrgsolve-0.9.0/mrgsolve/src/mrgsolve.cpp | 3 mrgsolve-0.9.0/mrgsolve/src/mrgsolve_init.cpp | 22 mrgsolve-0.9.0/mrgsolve/src/odepack_dlsoda.cpp | 2 mrgsolve-0.9.0/mrgsolve/src/odeproblem.cpp | 24 mrgsolve-0.9.0/mrgsolve/tests/testthat.R | 6 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-annot.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-as_data_set.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-as_list_mrgmod.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-cache.R | 6 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-carry-out.R | 14 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-carry_out.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-data_set.R | 43 - mrgsolve-0.9.0/mrgsolve/tests/testthat/test-deslist.R | 4 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-dplyr-generics.R | 18 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-env.R | 4 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-ev.R | 72 - mrgsolve-0.9.0/mrgsolve/tests/testthat/test-ev_assign.R | 6 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-ev_days.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-ev_rx.R |only mrgsolve-0.9.0/mrgsolve/tests/testthat/test-evid4.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-fixed-cmtn.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-idata_set.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-infusion.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-init.R |only mrgsolve-0.9.0/mrgsolve/tests/testthat/test-inventory-too.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-inventory.R | 22 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-iv-po.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-knobs.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-matlist.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-matrix.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-modspec.R | 41 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-mread.R |only mrgsolve-0.9.0/mrgsolve/tests/testthat/test-mrgindata.R | 14 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-mrgsim.R | 6 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-mrgsim_q.R |only mrgsolve-0.9.0/mrgsolve/tests/testthat/test-nmxml.R | 32 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-obsonly-obsaug.R | 10 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-opts.R | 22 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-param.R |only mrgsolve-0.9.0/mrgsolve/tests/testthat/test-rcpp_globals.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-realize.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-records.R | 4 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-relabel.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-rename.R | 16 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-rng.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-tad.R | 2 mrgsolve-0.9.0/mrgsolve/tests/testthat/test-update.R | 82 - mrgsolve-0.9.0/mrgsolve/tests/testthat/test-utils.R | 19 237 files changed, 3387 insertions(+), 2617 deletions(-)
Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in
a tidy workflow. 'landscapemetrics' reimplements the most common metrics from
'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>)
and new ones from the current literature on landscape metrics.
This package supports 'raster' spatial objects and takes
RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the
'raster' package as input arguments. It further provides utility functions
to visualize patches, select metrics and building blocks to develop new
metrics.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>),
Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>),
Sebastian Hanss [aut] (<https://orcid.org/0000-0002-3990-4897>),
Laura J. Graham [ctb] (Input on package structure),
Jeffrey Hollister [ctb] (Input on package structure),
Kimberly A. With [ctb] (Input on package structure),
Florian Privé [ctb] (Original author of underlying C++ code for
get_nearestneighbour() function),
Jeremy VanDerWal [ctb] (Original author of underlying C code for
get_patches() function),
Matt Strimas-Mackey [ctb] (Bugfix in sample_metrics())
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Diff between landscapemetrics versions 0.3 dated 2018-12-07 and 0.3.1 dated 2019-01-23
DESCRIPTION | 6 MD5 | 646 +-- NEWS.md | 107 R/calculate_lsm.R | 775 ++-- R/check_landscape.R | 310 - R/construct_buffer.R | 276 - R/data.R | 258 - R/extract_lsm.R | 696 +-- R/get_adjacencies.R | 160 R/get_boundaries.R | 212 - R/get_circumscribingcircle.R | 150 R/get_nearestneighbour.R | 150 R/get_patches.R | 582 +-- R/get_unique_values.R | 434 +- R/landscapemetrics-package.R | 103 R/list_lsm.R | 216 - R/lsm_c_ai.R | 294 - R/lsm_c_area_cv.R | 258 - R/lsm_c_area_mn.R | 260 - R/lsm_c_area_sd.R | 258 - R/lsm_c_cai_cv.R | 292 - R/lsm_c_cai_mn.R | 286 - R/lsm_c_cai_sd.R | 290 - R/lsm_c_circle_cv.R | 272 - R/lsm_c_circle_mn.R | 268 - R/lsm_c_circle_sd.R | 270 - R/lsm_c_clumpy.R | 334 - R/lsm_c_cohesion.R | 318 - R/lsm_c_contig_cv.R | 274 - R/lsm_c_contig_mn.R | 272 - R/lsm_c_contig_sd.R | 276 - R/lsm_c_core_cv.R | 284 - R/lsm_c_core_mn.R | 280 - R/lsm_c_core_sd.R | 284 - R/lsm_c_cpland.R | 316 - R/lsm_c_dcad.R | 312 - R/lsm_c_dcore_cv.R | 294 - R/lsm_c_dcore_mn.R | 288 - R/lsm_c_dcore_sd.R | 298 - R/lsm_c_division.R | 272 - R/lsm_c_ed.R | 316 - R/lsm_c_enn_cv.R | 284 - R/lsm_c_enn_mn.R | 286 - R/lsm_c_enn_sd.R | 286 - R/lsm_c_frac_cv.R | 264 - R/lsm_c_frac_mn.R | 258 - R/lsm_c_frac_sd.R | 262 - R/lsm_c_gyrate_cv.R | 272 - R/lsm_c_gyrate_mn.R | 270 - R/lsm_c_gyrate_sd.R | 270 - R/lsm_c_iji.R | 310 - R/lsm_c_lpi.R | 264 - R/lsm_c_lsi.R | 300 - R/lsm_c_mesh.R | 278 - R/lsm_c_ndca.R | 290 - R/lsm_c_nlsi.R | 338 - R/lsm_c_np.R | 260 - R/lsm_c_pafrac.R | 350 - R/lsm_c_para_cv.R | 258 - R/lsm_c_para_mn.R | 258 - R/lsm_c_para_sd.R | 258 - R/lsm_c_pd.R | 276 - R/lsm_c_pladj.R | 254 - R/lsm_c_pland.R | 248 - R/lsm_c_shape_cv.R | 264 - R/lsm_c_shape_mn.R | 264 - R/lsm_c_shape_sd.R | 264 - R/lsm_c_split.R | 270 - R/lsm_c_tca.R | 284 - R/lsm_c_te.R | 438 +- R/lsm_l_ai.R | 260 - R/lsm_l_area_cv.R | 258 - R/lsm_l_area_mn.R | 260 - R/lsm_l_area_sd.R | 258 - R/lsm_l_cai_cv.R | 320 - R/lsm_l_cai_mn.R | 314 - R/lsm_l_cai_sd.R | 318 - R/lsm_l_circle_cv.R | 266 - R/lsm_l_circle_mn.R | 266 - R/lsm_l_circle_sd.R | 270 - R/lsm_l_cohesion.R | 294 - R/lsm_l_condent.R | 312 - R/lsm_l_contag.R | 316 - R/lsm_l_contig_cv.R | 270 - R/lsm_l_contig_mn.R | 268 - R/lsm_l_contig_sd.R | 270 - R/lsm_l_core_cv.R | 314 - R/lsm_l_core_mn.R | 310 - R/lsm_l_core_sd.R | 312 - R/lsm_l_dcad.R | 334 - R/lsm_l_dcore_cv.R | 320 - R/lsm_l_dcore_mn.R | 314 - R/lsm_l_dcore_sd.R | 318 - R/lsm_l_division.R | 268 - R/lsm_l_ed.R | 308 - R/lsm_l_enn_cv.R | 276 - R/lsm_l_enn_mn.R | 276 - R/lsm_l_enn_sd.R | 276 - R/lsm_l_ent.R | 226 - R/lsm_l_frac_cv.R | 260 - R/lsm_l_frac_mn.R | 258 - R/lsm_l_frac_sd.R | 258 - R/lsm_l_gyrate_cv.R | 266 - R/lsm_l_gyrate_mn.R | 264 - R/lsm_l_gyrate_sd.R | 264 - R/lsm_l_iji.R | 314 - R/lsm_l_joinent.R | 296 - R/lsm_l_lpi.R | 256 - R/lsm_l_lsi.R | 296 - R/lsm_l_mesh.R | 266 - R/lsm_l_msidi.R | 268 - R/lsm_l_msiei.R | 258 - R/lsm_l_mutinf.R | 308 - R/lsm_l_ndca.R | 312 - R/lsm_l_np.R | 234 - R/lsm_l_pafrac.R | 340 - R/lsm_l_para_cv.R | 254 - R/lsm_l_para_mn.R | 254 - R/lsm_l_para_sd.R | 254 - R/lsm_l_pd.R | 280 - R/lsm_l_pladj.R | 246 - R/lsm_l_pr.R | 212 - R/lsm_l_prd.R | 254 - R/lsm_l_rpr.R | 274 - R/lsm_l_shape_cv.R | 264 - R/lsm_l_shape_mn.R | 264 - R/lsm_l_shape_sd.R | 264 - R/lsm_l_shdi.R | 240 - R/lsm_l_shei.R | 240 - R/lsm_l_sidi.R | 250 - R/lsm_l_siei.R | 252 - R/lsm_l_split.R | 268 - R/lsm_l_ta.R | 238 - R/lsm_l_tca.R | 308 - R/lsm_l_te.R | 334 - R/lsm_p_area.R | 308 - R/lsm_p_cai.R | 362 +- R/lsm_p_circle.R | 491 +- R/lsm_p_contig.R | 386 +- R/lsm_p_core.R | 427 +- R/lsm_p_enn.R | 606 +-- R/lsm_p_frac.R | 300 - R/lsm_p_gyrate.R | 417 +- R/lsm_p_ncore.R | 786 ++-- R/lsm_p_para.R | 284 - R/lsm_p_perim.R | 388 +- R/lsm_p_shape.R | 300 - R/matrix_to_raster.R | 164 R/onUnload.R | 16 R/options_landscapemetrics.R | 64 R/pad_raster.R | 246 - R/raster_to_points.R | 84 R/sample_lsm.R | 526 +- R/show_cores.R | 570 +-- R/show_correlation.R | 470 +- R/show_lsm.R | 602 +-- R/show_patches.R | 444 +- build/vignette.rds |binary inst/doc/getstarted.Rmd | 364 +- inst/doc/getstarted.html | 106 man/calculate_lsm.Rd | 11 man/get_adjacencies.Rd | 14 man/list_lsm.Rd | 5 man/sample_lsm.Rd | 61 src/Makevars |only src/Makevars.win |only tests/testthat.R | 8 tests/testthat/helper-brick.R | 8 tests/testthat/helper-landscapes.R | 34 tests/testthat/helper-points.R | 36 tests/testthat/test-calculate-lsm.R | 186 - tests/testthat/test-check-landscape.R | 44 tests/testthat/test-construct-buffer.R | 34 tests/testthat/test-extract-lsm.R | 66 tests/testthat/test-get-boundaries.R | 76 tests/testthat/test-get-circumscribungcircle.R | 60 tests/testthat/test-get-nearestneighbour.R | 36 tests/testthat/test-get-patches.R | 46 tests/testthat/test-get-unique-values.R | 166 tests/testthat/test-list-lsm.R | 92 tests/testthat/test-lsm-c-ai.R | 48 tests/testthat/test-lsm-c-area-cv.R | 48 tests/testthat/test-lsm-c-area-mn.R | 50 tests/testthat/test-lsm-c-area-sd.R | 48 tests/testthat/test-lsm-c-ca.R | 52 tests/testthat/test-lsm-c-cai-cv.R | 50 tests/testthat/test-lsm-c-cai-mn.R | 50 tests/testthat/test-lsm-c-cai-sd.R | 46 tests/testthat/test-lsm-c-circle-cv.R | 52 tests/testthat/test-lsm-c-circle-mn.R | 48 tests/testthat/test-lsm-c-circle-sd.R | 48 tests/testthat/test-lsm-c-clumpy.R | 48 tests/testthat/test-lsm-c-cohesion.R | 50 tests/testthat/test-lsm-c-contig-cv.R | 50 tests/testthat/test-lsm-c-contig-mn.R | 50 tests/testthat/test-lsm-c-contig-sd.R | 50 tests/testthat/test-lsm-c-core-cv.R | 46 tests/testthat/test-lsm-c-core-mn.R | 46 tests/testthat/test-lsm-c-core-sd.R | 46 tests/testthat/test-lsm-c-cpland.R | 48 tests/testthat/test-lsm-c-dcad.R | 48 tests/testthat/test-lsm-c-dcore_cv.R | 46 tests/testthat/test-lsm-c-dcore_mn.R | 46 tests/testthat/test-lsm-c-dcore_sd.R | 46 tests/testthat/test-lsm-c-division.R | 48 tests/testthat/test-lsm-c-ed.R | 48 tests/testthat/test-lsm-c-enn-cv.R | 46 tests/testthat/test-lsm-c-enn-mn.R | 46 tests/testthat/test-lsm-c-enn-sd.R | 46 tests/testthat/test-lsm-c-frac-cv.R | 46 tests/testthat/test-lsm-c-frac-mn.R | 46 tests/testthat/test-lsm-c-frac-sd.R | 46 tests/testthat/test-lsm-c-gyrate-cv.R | 46 tests/testthat/test-lsm-c-gyrate-mn.R | 46 tests/testthat/test-lsm-c-gyrate-sd.R | 46 tests/testthat/test-lsm-c-iji.R | 58 tests/testthat/test-lsm-c-lpi.R | 48 tests/testthat/test-lsm-c-lsi.R | 48 tests/testthat/test-lsm-c-mesh.R | 48 tests/testthat/test-lsm-c-ndca.R | 48 tests/testthat/test-lsm-c-nlsi.R | 48 tests/testthat/test-lsm-c-np.R | 48 tests/testthat/test-lsm-c-pafrac.R | 56 tests/testthat/test-lsm-c-para-cv.R | 46 tests/testthat/test-lsm-c-para-mn.R | 46 tests/testthat/test-lsm-c-para-sd.R | 46 tests/testthat/test-lsm-c-pd.R | 48 tests/testthat/test-lsm-c-pladj.R | 48 tests/testthat/test-lsm-c-pland.R | 48 tests/testthat/test-lsm-c-shape-cv.R | 46 tests/testthat/test-lsm-c-shape-mn.R | 46 tests/testthat/test-lsm-c-shape-sd.R | 46 tests/testthat/test-lsm-c-split.R | 48 tests/testthat/test-lsm-c-tca.R | 48 tests/testthat/test-lsm-c-te.R | 64 tests/testthat/test-lsm-l-ai.R | 48 tests/testthat/test-lsm-l-area-cv.R | 46 tests/testthat/test-lsm-l-area-mn.R | 50 tests/testthat/test-lsm-l-area-sd.R | 50 tests/testthat/test-lsm-l-cai-cv.R | 50 tests/testthat/test-lsm-l-cai-mn.R | 50 tests/testthat/test-lsm-l-cai-sd.R | 50 tests/testthat/test-lsm-l-circle-cv.R | 50 tests/testthat/test-lsm-l-circle-mn.R | 50 tests/testthat/test-lsm-l-circle-sd.R | 50 tests/testthat/test-lsm-l-cohesion.R | 48 tests/testthat/test-lsm-l-condent.R | 48 tests/testthat/test-lsm-l-contag.R | 56 tests/testthat/test-lsm-l-contig-cv.R | 46 tests/testthat/test-lsm-l-contig-mn.R | 46 tests/testthat/test-lsm-l-contig-sd.R | 46 tests/testthat/test-lsm-l-core-cv.R | 50 tests/testthat/test-lsm-l-core-mn.R | 50 tests/testthat/test-lsm-l-core-sd.R | 50 tests/testthat/test-lsm-l-dcad.R | 48 tests/testthat/test-lsm-l-dcore-cv.R | 50 tests/testthat/test-lsm-l-dcore-mn.R | 50 tests/testthat/test-lsm-l-dcore-sd.R | 50 tests/testthat/test-lsm-l-division.R | 48 tests/testthat/test-lsm-l-ed.R | 48 tests/testthat/test-lsm-l-enn-cv.R | 50 tests/testthat/test-lsm-l-enn-mn.R | 50 tests/testthat/test-lsm-l-enn-sd.R | 50 tests/testthat/test-lsm-l-ent.R | 48 tests/testthat/test-lsm-l-frac-cv.R | 46 tests/testthat/test-lsm-l-frac-mn.R | 46 tests/testthat/test-lsm-l-frac-sd.R | 46 tests/testthat/test-lsm-l-gyrate-cv.R | 46 tests/testthat/test-lsm-l-gyrate-mn.R | 46 tests/testthat/test-lsm-l-gyrate-sd.R | 48 tests/testthat/test-lsm-l-iji.R | 58 tests/testthat/test-lsm-l-joinent.R | 48 tests/testthat/test-lsm-l-lpi.R | 48 tests/testthat/test-lsm-l-lsi.R | 48 tests/testthat/test-lsm-l-mesh.R | 48 tests/testthat/test-lsm-l-msidi.R | 48 tests/testthat/test-lsm-l-msiei.R | 48 tests/testthat/test-lsm-l-mutinf.R | 48 tests/testthat/test-lsm-l-ndca.R | 48 tests/testthat/test-lsm-l-np.R | 48 tests/testthat/test-lsm-l-pafrac.R | 56 tests/testthat/test-lsm-l-para-cv.R | 46 tests/testthat/test-lsm-l-para-mn.R | 46 tests/testthat/test-lsm-l-para-sd.R | 46 tests/testthat/test-lsm-l-pd.R | 48 tests/testthat/test-lsm-l-pladj.R | 48 tests/testthat/test-lsm-l-pr.R | 48 tests/testthat/test-lsm-l-prd.R | 48 tests/testthat/test-lsm-l-rpr.R | 48 tests/testthat/test-lsm-l-shape-cv.R | 46 tests/testthat/test-lsm-l-shape-mn.R | 46 tests/testthat/test-lsm-l-shape-sd.R | 46 tests/testthat/test-lsm-l-shdi.R | 48 tests/testthat/test-lsm-l-shei.R | 48 tests/testthat/test-lsm-l-sidi.R | 48 tests/testthat/test-lsm-l-siei.R | 48 tests/testthat/test-lsm-l-split.R | 48 tests/testthat/test-lsm-l-ta.R | 48 tests/testthat/test-lsm-l-tca.R | 48 tests/testthat/test-lsm-l-te.R | 66 tests/testthat/test-lsm-p-area.R | 50 tests/testthat/test-lsm-p-cai.R | 46 tests/testthat/test-lsm-p-circle.R | 54 tests/testthat/test-lsm-p-contig.R | 50 tests/testthat/test-lsm-p-core.R | 61 tests/testthat/test-lsm-p-enn.R | 50 tests/testthat/test-lsm-p-frac.R | 50 tests/testthat/test-lsm-p-gyrate.R | 50 tests/testthat/test-lsm-p-nca.R | 50 tests/testthat/test-lsm-p-para.R | 50 tests/testthat/test-lsm-p-perim.R | 54 tests/testthat/test-lsm-p-shape.R | 48 tests/testthat/test-matrix-to-raster.R | 96 tests/testthat/test-pad-raster.R | 30 tests/testthat/test-raster-to-points.R | 32 tests/testthat/test-rcpp-get-coocurrence-matrix.R | 204 - tests/testthat/test-rcpp-get-entropy.R | 46 tests/testthat/test-sample-lsm.R | 104 tests/testthat/test-show-cores.R | 90 tests/testthat/test-show-correlation.R | 42 tests/testthat/test-show-lsm.R | 78 tests/testthat/test-show-patches.R | 70 tests/testthat/test-unique-values.R | 26 tests/testthat/test_fragstats.R | 3884 +++++++++++----------- vignettes/getstarted.Rmd | 364 +- 325 files changed, 29848 insertions(+), 29810 deletions(-)
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Title: Visualisations for Generalized Additive Models
Description: Extension of the 'mgcv' package, providing visual tools for Generalized Additive Models that exploit the additive structure of such models, scale to large data sets and can be used in conjunction with a wide range of response distributions. The focus is providing visual methods for better understanding the model output and for aiding model checking and development beyond simple exponential family regression. The graphical framework is based on the layering system provided by 'ggplot2'.
Author: Matteo Fasiolo [aut, cre],
Raphael Nedellec [aut],
Yannig Goude [ctb],
Simon N. Wood [ctb]
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between mgcViz versions 0.1.1 dated 2018-06-30 and 0.1.3 dated 2019-01-23
mgcViz-0.1.1/mgcViz/R/L_dens.R |only mgcViz-0.1.1/mgcViz/R/ggplotly_plotSmooth.R |only mgcViz-0.1.1/mgcViz/man/ggplotly.plotSmooth.Rd |only mgcViz-0.1.1/mgcViz/man/l_dens.Rd |only mgcViz-0.1.3/mgcViz/DESCRIPTION | 21 mgcViz-0.1.3/mgcViz/MD5 | 197 mgcViz-0.1.3/mgcViz/NAMESPACE | 47 mgcViz-0.1.3/mgcViz/R/I_compute_qq_gam.R | 2 mgcViz-0.1.3/mgcViz/R/I_createP.R | 9 mgcViz-0.1.3/mgcViz/R/I_discretize_qq_gam.R | 10 mgcViz-0.1.3/mgcViz/R/I_getDataTypeY.R |only mgcViz-0.1.3/mgcViz/R/I_getresidualsTransformSubsample.R |only mgcViz-0.1.3/mgcViz/R/I_plot_qq_gam.R | 8 mgcViz-0.1.3/mgcViz/R/I_prepareP.R | 3 mgcViz-0.1.3/mgcViz/R/I_preparePlotSmoothMD.R | 2 mgcViz-0.1.3/mgcViz/R/L_ciLine.R | 23 mgcViz-0.1.3/mgcViz/R/L_ciPoly.R | 23 mgcViz-0.1.3/mgcViz/R/L_dens1D.R |only mgcViz-0.1.3/mgcViz/R/L_dens2D.R |only mgcViz-0.1.3/mgcViz/R/L_densCheck.R | 53 mgcViz-0.1.3/mgcViz/R/L_fitContour.R | 2 mgcViz-0.1.3/mgcViz/R/L_fitDens.R |only mgcViz-0.1.3/mgcViz/R/L_fitLine.R | 25 mgcViz-0.1.3/mgcViz/R/L_fitPoints.R | 2 mgcViz-0.1.3/mgcViz/R/L_gridCheck1D.R | 32 mgcViz-0.1.3/mgcViz/R/L_gridCheck2D.R | 17 mgcViz-0.1.3/mgcViz/R/L_gridQCheck1D.R | 14 mgcViz-0.1.3/mgcViz/R/L_hist.R |only mgcViz-0.1.3/mgcViz/R/L_rug.R | 29 mgcViz-0.1.3/mgcViz/R/L_simLine.R |only mgcViz-0.1.3/mgcViz/R/L_vline.R |only mgcViz-0.1.3/mgcViz/R/add.R | 6 mgcViz-0.1.3/mgcViz/R/check0D.R |only mgcViz-0.1.3/mgcViz/R/check1D.R | 84 mgcViz-0.1.3/mgcViz/R/check2D.R | 109 mgcViz-0.1.3/mgcViz/R/gamV.R | 4 mgcViz-0.1.3/mgcViz/R/generic_functions.R | 1 mgcViz-0.1.3/mgcViz/R/getViz.R | 55 mgcViz-0.1.3/mgcViz/R/l_gridQCheck2D.R |only mgcViz-0.1.3/mgcViz/R/listLayers.R | 45 mgcViz-0.1.3/mgcViz/R/mqgamV.R | 3 mgcViz-0.1.3/mgcViz/R/plot.ptermInteraction.R |only mgcViz-0.1.3/mgcViz/R/plotDiff_mgcv_smooth_2D.R | 2 mgcViz-0.1.3/mgcViz/R/plotDiff_sos_smooth.R | 2 mgcViz-0.1.3/mgcViz/R/plotRGL_mgcv_smooth_2D.R | 3 mgcViz-0.1.3/mgcViz/R/plotSlice.R | 2 mgcViz-0.1.3/mgcViz/R/plot_gamViz.R | 6 mgcViz-0.1.3/mgcViz/R/plot_mgamViz.R | 30 mgcViz-0.1.3/mgcViz/R/plot_mgcv_smooth_1D.R | 30 mgcViz-0.1.3/mgcViz/R/plot_mgcv_smooth_2D.R | 7 mgcViz-0.1.3/mgcViz/R/plot_mgcv_smooth_MD.R | 3 mgcViz-0.1.3/mgcViz/R/plot_multi_mgcv_smooth_1D.R | 8 mgcViz-0.1.3/mgcViz/R/plot_multi_mgcv_smooth_2D.R | 18 mgcViz-0.1.3/mgcViz/R/plot_multi_ptermFactor.R | 15 mgcViz-0.1.3/mgcViz/R/plot_multi_ptermInteraction.R |only mgcViz-0.1.3/mgcViz/R/plot_multi_ptermNumeric.R | 9 mgcViz-0.1.3/mgcViz/R/plot_multi_random_effect.R | 13 mgcViz-0.1.3/mgcViz/R/plot_ptermNumeric.R | 2 mgcViz-0.1.3/mgcViz/R/plot_sos_smooth.R | 5 mgcViz-0.1.3/mgcViz/R/postSim.R |only mgcViz-0.1.3/mgcViz/R/print_plotGam.R | 46 mgcViz-0.1.3/mgcViz/R/print_plotSmooth.R | 19 mgcViz-0.1.3/mgcViz/R/pterm.R | 32 mgcViz-0.1.3/mgcViz/R/qgamV.R | 2 mgcViz-0.1.3/mgcViz/R/qq_gamViz.R | 31 mgcViz-0.1.3/mgcViz/R/qqplots.R | 5 mgcViz-0.1.3/mgcViz/R/shine.qqGam.R | 83 mgcViz-0.1.3/mgcViz/R/simulate_gam.R | 70 mgcViz-0.1.3/mgcViz/R/sm.R | 10 mgcViz-0.1.3/mgcViz/R/utilities.R | 5 mgcViz-0.1.3/mgcViz/R/zoom_qqGam.R | 16 mgcViz-0.1.3/mgcViz/R/zzz.R | 2 mgcViz-0.1.3/mgcViz/inst/CITATION | 29 mgcViz-0.1.3/mgcViz/inst/doc/mgcviz.R | 35 mgcViz-0.1.3/mgcViz/inst/doc/mgcviz.html | 3351 ++++++++++++++- mgcViz-0.1.3/mgcViz/inst/doc/mgcviz.rmd | 93 mgcViz-0.1.3/mgcViz/man/check0D.Rd |only mgcViz-0.1.3/mgcViz/man/check1D.Rd | 33 mgcViz-0.1.3/mgcViz/man/check2D.Rd | 33 mgcViz-0.1.3/mgcViz/man/gamV.Rd | 4 mgcViz-0.1.3/mgcViz/man/getViz.Rd | 14 mgcViz-0.1.3/mgcViz/man/l_dens1D.Rd |only mgcViz-0.1.3/mgcViz/man/l_dens2D.Rd |only mgcViz-0.1.3/mgcViz/man/l_densCheck.Rd | 43 mgcViz-0.1.3/mgcViz/man/l_fitDens.Rd |only mgcViz-0.1.3/mgcViz/man/l_fitLine.Rd | 2 mgcViz-0.1.3/mgcViz/man/l_gridCheck1D.Rd | 6 mgcViz-0.1.3/mgcViz/man/l_gridCheck2D.Rd | 2 mgcViz-0.1.3/mgcViz/man/l_gridQCheck1D.Rd | 7 mgcViz-0.1.3/mgcViz/man/l_gridQCheck2D.Rd |only mgcViz-0.1.3/mgcViz/man/l_hist.Rd |only mgcViz-0.1.3/mgcViz/man/l_simLine.Rd |only mgcViz-0.1.3/mgcViz/man/l_vline.Rd |only mgcViz-0.1.3/mgcViz/man/mqgamV.Rd | 3 mgcViz-0.1.3/mgcViz/man/plot.gamViz.Rd | 2 mgcViz-0.1.3/mgcViz/man/plot.mgamViz.Rd | 28 mgcViz-0.1.3/mgcViz/man/plot.mgcv.smooth.1D.Rd | 20 mgcViz-0.1.3/mgcViz/man/plot.mgcv.smooth.2D.Rd | 3 mgcViz-0.1.3/mgcViz/man/plot.ptermInteraction.Rd |only mgcViz-0.1.3/mgcViz/man/plot.sos.smooth.Rd | 5 mgcViz-0.1.3/mgcViz/man/plotDiff.mgcv.smooth.2D.Rd | 2 mgcViz-0.1.3/mgcViz/man/plotDiff.sos.smooth.Rd | 2 mgcViz-0.1.3/mgcViz/man/plotSlice.Rd | 5 mgcViz-0.1.3/mgcViz/man/postSim.Rd |only mgcViz-0.1.3/mgcViz/man/print.plotSmooth.Rd | 6 mgcViz-0.1.3/mgcViz/man/pterm.Rd | 3 mgcViz-0.1.3/mgcViz/man/qgamV.Rd | 2 mgcViz-0.1.3/mgcViz/man/qq.gamViz.Rd | 20 mgcViz-0.1.3/mgcViz/man/qqplots.Rd | 5 mgcViz-0.1.3/mgcViz/man/simulate.gam.Rd | 17 mgcViz-0.1.3/mgcViz/man/zoom.qqGam.Rd | 6 mgcViz-0.1.3/mgcViz/man/zto1.Rd | 4 mgcViz-0.1.3/mgcViz/vignettes/mgcviz.rmd | 93 113 files changed, 4454 insertions(+), 726 deletions(-)
Title: The R to MOSEK Optimization Interface
Description: This is a generic meta-package designed to make the optimization
facilities of MOSEK available from the R-language. The interface supports
large-scale optimization of many kinds: Mixed-integer and continuous linear,
second-order cone, exponential cone and power cone optimization, as well as
continuous semidefinite optimization. Rmosek and the R-language are
open-source projects. MOSEK is a proprietary product, but
unrestricted trial and academic licenses are available.
Author: MOSEK ApS
Maintainer: Henrik A. Friberg <haf@mosek.com>
Diff between Rmosek versions 1.3.0 dated 2019-01-18 and 1.3.1 dated 2019-01-23
DESCRIPTION | 6 +-- MD5 | 10 +++-- NAMESPACE | 6 +++ NEWS | 8 ++++ R/export.R |only man/export.Rd |only man/mosek_attachbuilder.Rd | 80 +++++++++++++++++++++++++-------------------- 7 files changed, 68 insertions(+), 42 deletions(-)
Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a common interface for model fitting, prediction, performance assessment, and presentation of results. Supports predictive modeling of numerical, categorical, and censored time-to-event outcomes and resample (bootstrap and cross-validation) estimation of model performance.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between MachineShop versions 1.0.0 dated 2019-01-02 and 1.1.0 dated 2019-01-23
DESCRIPTION | 20 - MD5 | 195 ++++++------ NAMESPACE | 3 NEWS.md | 11 R/AllClasses.R | 73 +++- R/ML_AdaBagModel.R | 11 R/ML_AdaBoostModel.R | 14 R/ML_BARTMachineModel.R | 15 R/ML_BARTModel.R |only R/ML_BlackBoostModel.R | 30 + R/ML_C50Model.R | 12 R/ML_CForestModel.R | 30 + R/ML_CoxModel.R | 18 - R/ML_EarthModel.R | 15 R/ML_FDAModel.R | 23 + R/ML_GAMBoostModel.R | 29 + R/ML_GBMModel.R | 38 +- R/ML_GLMBoostModel.R | 29 + R/ML_GLMModel.R | 4 R/ML_GLMNetModel.R | 43 +- R/ML_KNNModel.R | 18 + R/ML_LARSModel.R | 10 R/ML_LDAModel.R | 10 R/ML_LMModel.R | 2 R/ML_MDAModel.R | 10 R/ML_NNetModel.R | 11 R/ML_NaiveBayesModel.R | 2 R/ML_PLSModel.R | 10 R/ML_POLRModel.R | 2 R/ML_QDAModel.R | 2 R/ML_RPartModel.R | 27 + R/ML_RandomForestModel.R | 13 R/ML_RangerModel.R | 25 + R/ML_SVMModel.R | 40 ++ R/ML_SurvRegModel.R | 8 R/ML_TreeModel.R | 2 R/ML_XGBModel.R | 70 ++++ R/MachineShop-package.R | 3 R/calibration.R | 4 R/confusion.R | 74 ++++ R/fit.R | 6 R/grid.R |only R/metricinfo.R | 2 R/metrics.R | 486 ++++++++++++++++++++++++------- R/modelinfo.R | 9 R/performance.R | 23 + R/plots.R | 11 R/predict.R | 6 R/resample.R | 6 R/show.R | 14 R/summary.R | 2 R/survival.R |only R/tune.R | 96 ++++-- R/utils.R | 67 +++- README.md | 101 +++++- inst/doc/Introduction.R | 2 inst/doc/Introduction.Rmd | 2 inst/doc/Introduction.html | 149 +++++---- inst/doc/MLModels.Rmd | 2 inst/doc/MLModels.html | 6 man/AdaBagModel.Rd | 3 man/AdaBoostModel.Rd | 4 man/BARTMachineModel.Rd | 5 man/BARTModel.Rd |only man/BlackBoostModel.Rd | 3 man/C50Model.Rd | 3 man/CForestModel.Rd | 3 man/EarthModel.Rd | 4 man/FDAModel.Rd | 7 man/GAMBoostModel.Rd | 3 man/GBMModel.Rd | 5 man/GLMBoostModel.Rd | 3 man/GLMNetModel.Rd | 7 man/Grid.Rd |only man/KNNModel.Rd | 4 man/LARSModel.Rd | 3 man/LDAModel.Rd | 3 man/MDAModel.Rd | 3 man/MLModel.Rd | 27 + man/MachineShop-package.Rd | 3 man/NNetModel.Rd | 3 man/PLSModel.Rd | 3 man/RPartModel.Rd | 3 man/RandomForestModel.Rd | 4 man/RangerModel.Rd | 4 man/SVMModel.Rd | 10 man/XGBModel.Rd | 12 man/confusion.Rd | 15 man/figures/README-unnamed-chunk-9-1.png |binary man/fit-methods.Rd | 4 man/metrics.Rd | 70 ++-- man/modelinfo.Rd | 5 man/performance.Rd | 18 - man/predict.Rd | 6 man/resample-methods.Rd | 6 man/tune-methods.Rd | 51 ++- tests/testthat/Rplots.pdf |binary tests/testthat/helper-models.R | 1 tests/testthat/test-ML_BARTModel.R |only tests/testthat/test-tune_grid.R |only vignettes/Introduction.Rmd | 2 vignettes/MLModels.Rmd | 2 102 files changed, 1662 insertions(+), 596 deletions(-)
Title: Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
Description: Extends the fitdistr() function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available. See e.g. Casella & Berger (2002). Statistical inference. Pacific Grove.
Author: Marie-Laure Delignette-Muller [aut],
Christophe Dutang [aut],
Regis Pouillot [ctb],
Jean-Baptiste Denis [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between fitdistrplus versions 1.0-11 dated 2018-09-10 and 1.0-14 dated 2019-01-23
DESCRIPTION | 17 - MD5 | 62 ++-- R/cdfcompcens.R | 4 R/detectbound.R | 5 R/fitdistcens.R | 5 R/plotdistcens.R | 674 ++++++++++++++++++++++----------------------- R/prefit.R | 2 R/qmedist.R | 4 R/qqcompcens.R | 556 ++++++++++++++++++------------------- R/util-checkparamlist.R | 12 R/util-getparam.R | 7 R/util-testdensity.R | 14 build/vignette.rds |binary data/danishmulti.rda |binary data/danishuni.rda |binary data/dataFAQlog1.rda |binary data/dataFAQscale1.rda |binary data/dataFAQscale2.rda |binary data/endosulfan.rda |binary data/fluazinam.rda |binary data/groundbeef.rda |binary data/salinity.rda |binary data/smokedfish.rda |binary data/toxocara.rda |binary inst/NEWS | 6 inst/doc/FAQ.R |only inst/doc/FAQ.html | 98 ++++-- inst/doc/Optimalgo.R |only inst/doc/Optimalgo.html | 126 ++++---- inst/doc/paper2JSS.pdf |binary tests/t-detectbound.R | 7 tests/t-fitdistcens.R | 185 ++++++------ tests/t-util-testdensity.R | 12 33 files changed, 948 insertions(+), 848 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-11 1.3.1
2018-11-28 1.3.0
2018-07-22 1.2.0
2018-07-02 1.1.1
2018-07-01 1.1.0
2018-05-29 1.0
Title: Exploring the Phylogenetic Signal in Continuous Traits
Description: A collection of tools to explore the phylogenetic signal in univariate and multivariate data. The package provides functions to plot traits data against a phylogenetic tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method.
Author: Francois Keck <francois.keck@gmail.com>
Maintainer: ORPHANED
Diff between phylosignal versions 1.2 dated 2018-01-10 and 1.2.1 dated 2019-01-23
DESCRIPTION | 11 MD5 | 20 - build/vignette.rds |binary inst/doc/Basics.R | 102 +++---- inst/doc/Basics.Rmd | 2 inst/doc/Basics.html | 562 +++++++++++++++++++++++++++++++------------- inst/doc/Demo_plots.R | 162 ++++++------ inst/doc/Demo_plots.Rmd | 4 inst/doc/Demo_plots.html | 600 ++++++++++++++++++++++++++++++++--------------- vignettes/Basics.Rmd | 2 vignettes/Demo_plots.Rmd | 4 11 files changed, 966 insertions(+), 503 deletions(-)
Title: Tools for Eurostat Open Data
Description: Tools to download data from the Eurostat database
<http://ec.europa.eu/eurostat> together with search and
manipulation utilities.
Author: Leo Lahti [aut, cre],
Janne Huovari [aut],
Markus Kainu [aut],
Przemyslaw Biecek [aut],
Joona Lehtomaki [ctb],
Francois Briatte [ctb],
Oliver Reiter [ctb]
Maintainer: ORPHANED
Diff between eurostat versions 3.3.1 dated 2018-11-24 and 3.3.1.1 dated 2019-01-23
eurostat-3.3.1.1/eurostat/DESCRIPTION | 11 eurostat-3.3.1.1/eurostat/MD5 | 28 +- eurostat-3.3.1.1/eurostat/build/vignette.rds |binary eurostat-3.3.1.1/eurostat/inst/doc/blogposts.html | 188 +++++++++++++- eurostat-3.3.1.1/eurostat/inst/doc/cheatsheet.html | 188 +++++++++++++- eurostat-3.3.1.1/eurostat/inst/doc/eurostat_tutorial.html |only eurostat-3.3.1.1/eurostat/inst/doc/publications.Rmd | 2 eurostat-3.3.1.1/eurostat/inst/doc/publications.html | 188 +++++++++++++- eurostat-3.3.1.1/eurostat/vignettes/fig/map1ex-1.png |binary eurostat-3.3.1.1/eurostat/vignettes/fig/maps2-1.png |binary eurostat-3.3.1.1/eurostat/vignettes/fig/maps3-1.png |binary eurostat-3.3.1.1/eurostat/vignettes/fig/maps4-1.png |binary eurostat-3.3.1.1/eurostat/vignettes/fig/plotGallery-1.png |binary eurostat-3.3.1.1/eurostat/vignettes/fig/trains_plot-1.png |binary eurostat-3.3.1.1/eurostat/vignettes/publications.Rmd | 2 eurostat-3.3.1/eurostat/vignettes/eurostat_tutorial.html |only 16 files changed, 578 insertions(+), 29 deletions(-)
Title: Tools to Work with Survey Data
Description: Data obtained from surveys contains information not only about the
survey responses, but also the survey metadata, e.g. the original survey
questions and the answer options. The 'surveydata' package makes it easy to
keep track of this metadata, and to easily extract columns with
specific questions.
Author: Andrie de Vries [aut, cre, cph]
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between surveydata versions 0.2.2 dated 2018-12-06 and 0.2.3 dated 2019-01-23
DESCRIPTION | 8 MD5 | 111 ++++----- NAMESPACE | 2 NEWS | 26 ++ R/cleandata.R | 127 +++++----- R/dplyr_verbs.R | 61 +++-- R/encoding.R | 43 +-- R/extract.R | 116 ++++----- R/merge.R | 27 +- R/opentext.R | 67 ++--- R/pattern.R | 19 - R/plots.R | 104 ++++---- R/questions.R | 121 +++++----- R/strings.R | 128 +++++----- R/surveydata-deprecated.R | 39 +-- R/surveydata-package.R | 41 +-- R/surveydata.R | 65 ++--- R/tools.R | 11 R/varlabels.R | 15 - build/vignette.rds |binary inst/doc/surveydata.R | 28 +- inst/doc/surveydata.Rmd | 2 inst/doc/surveydata.html | 88 ++++--- inst/examples/example-dplyr-verbs.R |only inst/vignette_child/child.Rmd | 36 +-- inst/vignette_child/child.html | 416 +++++++++++++++++++++++++++-------- man/Extract.Rd | 8 man/as.surveydata.Rd | 2 man/dplyr-surveydata.Rd | 20 + man/dropout.Rd | 2 man/encToInt.Rd | 2 man/names.Rd | 6 man/pattern.Rd | 2 man/question_text_common.Rd | 2 man/question_text_unique.Rd | 2 man/questions.Rd | 2 man/strCommonUnique.Rd | 2 man/surveydata-deprecated.Rd | 2 man/which.q.Rd | 2 tests/testthat/helper.R | 80 +++--- tests/testthat/notest-9-gss.R | 68 +++-- tests/testthat/test-01-essentials.R | 20 - tests/testthat/test-01-surveydata.R | 163 ++++++------- tests/testthat/test-02-whichq.R | 70 ++--- tests/testthat/test-03-extract.R | 204 ++++++++--------- tests/testthat/test-03-replace.R | 129 +++++----- tests/testthat/test-03-strings.R | 68 ++--- tests/testthat/test-04-merge.R | 97 ++++---- tests/testthat/test-05-questions.R | 155 ++++++------- tests/testthat/test-06-encoding.R | 19 - tests/testthat/test-08-tools.R | 10 tests/testthat/test-09-dplyr-verbs.R | 6 tests/testthat/test-10-cleandata.R | 11 tests/testthat/test-11-encoding.R | 8 tests/testthat/test-12-plots.R | 10 tests/testthat/test-13-opentext.R | 8 vignettes/surveydata.Rmd | 2 57 files changed, 1589 insertions(+), 1294 deletions(-)
Title: Simulate Temporally Autocorrelated Populations
Description: Temporally autocorrelated populations are correlated in their vital rates (growth, death, etc.) from year to year. It is very common for populations, whether they be bacteria, plants, or humans, to be temporally autocorrelated. This poses a challenge for stochastic population modeling, because a temporally correlated population will behave differently from an uncorrelated one.
This package provides tools for simulating populations with white noise (no temporal autocorrelation), red noise (positive temporal autocorrelation), and blue noise (negative temporal autocorrelation). The algebraic formulation for autocorrelated noise comes from Ruokolainen et al. (2009) <doi:10.1016/j.tree.2009.04.009>. Models for unstructured populations and for structured populations (matrix models) are available.
Author: Julia Pilowsky [aut, cre] (<https://orcid.org/0000-0002-6376-2585>)
Maintainer: Julia Pilowsky <jap2178@caa.columbia.edu>
Diff between colorednoise versions 1.0.3 dated 2018-06-01 and 1.0.4 dated 2019-01-23
DESCRIPTION | 22 +++++---- MD5 | 28 ++++++------ NAMESPACE | 2 NEWS.md | 4 + R/colorednoise.R | 1 R/simulate_populations.R | 9 ++- build/vignette.rds |binary inst/doc/noise.html | 88 +++++++++++++++++++++++--------------- man/autocorr_sim.Rd | 4 - man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/matrix_model.Rd | 4 - src/Makevars | 2 src/Makevars.win | 2 tests/testthat/test_simulations.R | 2 15 files changed, 101 insertions(+), 67 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-03-31 1.0.0
2015-06-16 0.99.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-04-18 1.2.0
2016-05-30 1.1.1
2016-02-29 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-23 1.1-1
2016-02-06 1.0-2
2016-02-02 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-06-05 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-24 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-06-28 0.9.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-16 2.0.0
2016-04-16 1.0.2
2015-08-13 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-16 3.0.0
2016-07-26 2.6.0
2016-03-04 2.4.3
2015-08-13 2.3.1
2015-07-07 2.3.0
2015-04-14 2.2.0
2015-02-17 2.1.1
2014-12-18 2.1.0
2014-12-03 2.0.2
2014-11-24 2.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-05-24 1.1
2016-05-23 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-22 0.2
2018-03-28 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-04-28 2.1.3
2017-03-15 2.1.2
2017-02-22 2.1.0
2016-08-03 2.0.3
2016-02-16 2.0.2
2016-01-27 2.0.1
2015-08-13 2.0
Title: Data Sets from Ramsey and Schafer's "Statistical Sleuth (3rd
Ed)"
Description: Data sets from Ramsey, F.L. and Schafer, D.W. (2013), "The
Statistical Sleuth: A Course in Methods of Data Analysis (3rd
ed)", Cengage Learning.
Author: Original by F.L. Ramsey and D.W. Schafer;
modifications by Daniel W. Schafer, Jeannie Sifneos and Berwin
A. Turlach; vignettes contributed by Nicholas Horton, Linda Loi,
Kate Aloisio and Ruobing Zhang, with corrections by Randall Pruim
Maintainer: ORPHANED
Diff between Sleuth3 versions 1.0-2 dated 2016-06-15 and 1.0-2.1 dated 2019-01-23
DESCRIPTION | 11 ++++--- MD5 | 53 +++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/chapter01-HortonMosaic.R |only inst/doc/chapter01-HortonMosaic.pdf |binary inst/doc/chapter02-HortonMosaic.R |only inst/doc/chapter02-HortonMosaic.pdf |binary inst/doc/chapter03-HortonMosaic.R |only inst/doc/chapter03-HortonMosaic.pdf |binary inst/doc/chapter04-HortonMosaic.R |only inst/doc/chapter04-HortonMosaic.pdf |binary inst/doc/chapter05-HortonMosaic.R |only inst/doc/chapter05-HortonMosaic.pdf |binary inst/doc/chapter06-HortonMosaic.R |only inst/doc/chapter06-HortonMosaic.pdf |binary inst/doc/chapter07-HortonMosaic.R |only inst/doc/chapter07-HortonMosaic.pdf |binary inst/doc/chapter08-HortonMosaic.R |only inst/doc/chapter08-HortonMosaic.pdf |binary inst/doc/chapter09-HortonMosaic.R |only inst/doc/chapter09-HortonMosaic.pdf |binary inst/doc/chapter10-HortonMosaic.R |only inst/doc/chapter10-HortonMosaic.pdf |binary inst/doc/chapter11-HortonMosaic.R |only inst/doc/chapter11-HortonMosaic.Rnw | 2 - inst/doc/chapter11-HortonMosaic.pdf |binary inst/doc/chapter12-HortonMosaic.R |only inst/doc/chapter12-HortonMosaic.Rnw | 1 inst/doc/chapter12-HortonMosaic.pdf |binary inst/doc/chapter13-HortonMosaic.R |only inst/doc/chapter13-HortonMosaic.pdf |binary man/ex1029.Rd | 4 +- vignettes/chapter11-HortonMosaic.Rnw | 2 - vignettes/chapter12-HortonMosaic.Rnw | 1 34 files changed, 46 insertions(+), 28 deletions(-)
Title: Data Sets from Ramsey and Schafer's "Statistical Sleuth (2nd
Ed)"
Description: Data sets from Ramsey, F.L. and Schafer, D.W. (2002), "The
Statistical Sleuth: A Course in Methods of Data Analysis (2nd
ed)", Duxbury.
Author: Original by F.L. Ramsey and D.W. Schafer;
modifications by Daniel W. Schafer, Jeannie Sifneos and Berwin
A. Turlach; vignettes contributed by Nicholas Horton, Kate Aloisio
and Ruobing Zhang, with corrections by Randall Pruim
Maintainer: ORPHANED
Diff between Sleuth2 versions 2.0-4 dated 2016-06-15 and 2.0-4.1 dated 2019-01-23
DESCRIPTION | 11 +++++-- MD5 | 49 ++++++++++++++++++++++------------- build/vignette.rds |binary inst/doc/chapter01-HortonMosaic.R |only inst/doc/chapter01-HortonMosaic.pdf |binary inst/doc/chapter02-HortonMosaic.R |only inst/doc/chapter02-HortonMosaic.pdf |binary inst/doc/chapter03-HortonMosaic.R |only inst/doc/chapter03-HortonMosaic.pdf |binary inst/doc/chapter04-HortonMosaic.R |only inst/doc/chapter04-HortonMosaic.pdf |binary inst/doc/chapter05-HortonMosaic.R |only inst/doc/chapter05-HortonMosaic.pdf |binary inst/doc/chapter06-HortonMosaic.R |only inst/doc/chapter06-HortonMosaic.pdf |binary inst/doc/chapter07-HortonMosaic.R |only inst/doc/chapter07-HortonMosaic.pdf |binary inst/doc/chapter08-HortonMosaic.R |only inst/doc/chapter08-HortonMosaic.pdf |binary inst/doc/chapter09-HortonMosaic.R |only inst/doc/chapter09-HortonMosaic.pdf |binary inst/doc/chapter10-HortonMosaic.R |only inst/doc/chapter10-HortonMosaic.pdf |binary inst/doc/chapter11-HortonMosaic.R |only inst/doc/chapter11-HortonMosaic.pdf |binary inst/doc/chapter12-HortonMosaic.R |only inst/doc/chapter12-HortonMosaic.Rnw | 1 inst/doc/chapter12-HortonMosaic.pdf |binary inst/doc/chapter13-HortonMosaic.R |only inst/doc/chapter13-HortonMosaic.pdf |binary man/ex1029.Rd | 4 +- vignettes/chapter12-HortonMosaic.Rnw | 1 32 files changed, 42 insertions(+), 24 deletions(-)
Title: Handling Missing Values with Multivariate Data Analysis
Description: Imputation of incomplete continuous or categorical datasets; Missing values are imputed with a principal component analysis (PCA), a multiple correspondence analysis (MCA) model or a multiple factor analysis (MFA) model; Perform multiple imputation with and in PCA or MCA.
Author: Francois Husson, Julie Josse
Maintainer: Francois Husson <husson@agrocampus-ouest.fr>
Diff between missMDA versions 1.13 dated 2018-06-25 and 1.14 dated 2019-01-23
DESCRIPTION | 15 +-- MD5 | 56 +++++++------ NAMESPACE | 7 + R/MIFAMD.R |only R/MIMCA.R | 3 R/MIPCA.R | 3 R/estim_ncpFAMD.R | 3 R/estim_ncpMCA.R | 4 R/estim_ncpMultilevel.R |only R/imputeFAMD.R | 1 R/imputeMCA.R | 189 ++++++++++++++++++++++----------------------- R/imputeMFA.R | 2 R/imputeMultilevel.R | 47 +++++------ R/prelim.R | 23 +++-- build/vignette.rds |binary man/MIFAMD.Rd |only man/MIMCA.Rd | 2 man/MIPCA.Rd | 3 man/estim_ncpFAMD.Rd | 2 man/estim_ncpMCA.Rd | 2 man/estim_ncpMultilevel.Rd |only man/estim_ncpPCA.Rd | 2 man/imputeCA.Rd | 4 man/imputeFAMD.Rd | 2 man/imputeMCA.Rd | 4 man/imputeMFA.Rd | 2 man/imputeMultilevel.Rd | 2 man/imputePCA.Rd | 2 man/plot.MIMCA.Rd | 2 man/plot.MIPCA.Rd | 2 man/prelim.Rd | 8 - 31 files changed, 205 insertions(+), 187 deletions(-)
Title: Image Processing Library Based on 'CImg'
Description: Fast image processing for images in up to 4 dimensions (two spatial
dimensions, one time/depth dimension, one colour dimension). Provides most
traditional image processing tools (filtering, morphology, transformations,
etc.) as well as various functions for easily analysing image data using R. The
package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image
processing.
Author: Simon Barthelme [aut, cre],
David Tschumperle [ctb],
Jan Wijffels [ctb],
Haz Edine Assemlal [ctb]
Maintainer: ORPHANED
Diff between imager versions 0.41.1 dated 2018-05-30 and 0.41.2 dated 2019-01-23
DESCRIPTION | 12 MD5 | 18 build/vignette.rds |binary inst/doc/gettingstarted.html | 1500 +++++++++++++++++++------------------------ inst/doc/pixsets.R | 2 inst/doc/pixsets.Rmd | 2 inst/doc/pixsets.html | 1074 +++++++++++++++--------------- src/Makevars.in | 3 src/Makevars.win | 5 vignettes/pixsets.Rmd | 2 10 files changed, 1272 insertions(+), 1346 deletions(-)
Title: Get WHO Tuberculosis Data
Description: Facilitates easy import of analysis ready World Health Organisation Tuberculosis data and provides plotting functions for exploratory data analysis.
Author: Sam Abbott [aut, cre] (<https://orcid.org/0000-0001-8057-8037>)
Maintainer: Sam Abbott <contact@samabbott.co.uk>
Diff between getTBinR versions 0.5.6 dated 2018-11-15 and 0.5.7 dated 2019-01-23
DESCRIPTION | 9 - MD5 | 80 ++++++----- NAMESPACE | 5 NEWS.md | 36 ++++- R/get_tb_burden.R | 3 R/map_tb_burden.R | 12 + R/plot_tb_burden.R | 34 ++++ R/plot_tb_burden_overview.R | 6 R/plot_tb_burden_summary.R |only R/render_country_report.R |only R/summarise_tb_burden.R | 162 ++++++++++++++++------- README.md | 91 +++++++++--- build/vignette.rds |binary inst/doc/case_fatality_rate.Rmd | 4 inst/doc/case_fatality_rate.html | 84 ++++++++--- inst/doc/case_study_global_trends.Rmd | 2 inst/doc/case_study_global_trends.html | 40 ++++- inst/doc/intro.R | 6 inst/doc/intro.Rmd | 17 +- inst/doc/intro.html | 125 +++++++++++------ inst/rmarkdown |only inst/scripts |only inst/shiny/ExploreGlobalTB/rsconnect |only inst/shiny/ExploreGlobalTB/server.R | 9 + inst/shiny/ExploreGlobalTB/ui.R | 10 - man/figure/logo.png |only man/figure/map-tb-incidence-eur-1.png |binary man/figure/plot-tb-incidence-eur-1.png |binary man/figure/plot-tb-incidence-eur-per-1.png |binary man/figure/plot-tb-incidence-uk-1.png |binary man/figure/plot-tb-incidence-uk-compare-1.png |only man/img/ExampleCountryReport.png |only man/img/ExploreGlobalTB.png |binary man/map_tb_burden.Rd | 14 + man/plot_tb_burden.Rd | 25 ++- man/plot_tb_burden_overview.Rd | 13 + man/plot_tb_burden_summary.Rd |only man/render_country_report.Rd |only man/summarise_tb_burden.Rd | 39 +++-- tests/test-files/summarise_tb_burden/test-10.rds |only tests/test-files/summarise_tb_burden/test-11.rds |only tests/test-files/summarise_tb_burden/test-12.rds |only tests/testthat/test-plot_tb_burden.R | 9 + tests/testthat/test-plot_tb_burden_summary.R |only tests/testthat/test-summarise_tb_burden.R | 44 ++++++ vignettes/case_fatality_rate.Rmd | 4 vignettes/case_study_global_trends.Rmd | 2 vignettes/intro.Rmd | 17 +- 48 files changed, 646 insertions(+), 256 deletions(-)
Title: Moran's Eigenvector-Based Spatial Regression Models
Description: Functions for estimating Moran's eigenvector-based
spatial regression models.
For details see Murakami (2018) <arXiv:1703.04467>.
Author: Daisuke Murakami
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>
Diff between spmoran versions 0.1.6 dated 2018-10-06 and 0.1.6.1 dated 2019-01-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/predict0.R | 2 +- build/vignette.rds |binary man/predict0.Rd | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-)
Title: R Logging Package
Description: Pure R implementation of the ubiquitous log4j package. It offers hierarchic
loggers, multiple handlers per logger, level based filtering, space handling in messages
and custom formatting.
Author: Mario Frasca [aut],
Walerian Sokolowski [cre]
Maintainer: Walerian Sokolowski <r-logging@wlogsolutions.com>
Diff between logging versions 0.9-105 dated 2019-01-16 and 0.9-106 dated 2019-01-23
logging-0.9-105/logging/tests/test.automatic-format.R |only logging-0.9-105/logging/tests/test.data.interaction.R |only logging-0.9-105/logging/tests/test.handlers.R |only logging-0.9-106/logging/DESCRIPTION | 8 ++++---- logging-0.9-106/logging/MD5 | 14 ++++++++------ logging-0.9-106/logging/NEWS.md | 6 ++++++ logging-0.9-106/logging/R/oo.R | 15 ++++++++++++++- logging-0.9-106/logging/tests/testthat |only logging-0.9-106/logging/tests/testthat.R |only 9 files changed, 32 insertions(+), 11 deletions(-)
Title: Structural Bayesian Vector Autoregression Models
Description: Provides a function for running Structural Bayesian Vector Autoregression models with the method developed by Baumeister and Hamilton (2015) <doi:10.3982/ECTA12356>, Baumeister and Hamilton (2017) <doi:10.3386/w24167>, and Baumeister and Hamilton (2018) <doi:10.1016/j.jmoneco.2018.06.005>. Functions for plotting impulse responses, historical decompositions, and posterior distributions of model parameters are also provided.
Author: Paul Richardson
Maintainer: Paul Richardson <p.richardson.54391@gmail.com>
Diff between BHSBVAR versions 1.0.0 dated 2018-11-19 and 1.0.1 dated 2019-01-23
DESCRIPTION | 12 MD5 | 38 +- R/BHSBVAR.R | 372 +++++++++++++++------------- R/RcppExports.R | 24 - build/vignette.rds |binary inst/doc/BHSBVAR.R | 75 ++--- inst/doc/BHSBVAR.Rnw | 229 +++++++++-------- inst/doc/BHSBVAR.pdf |binary man/BH_SBVAR.Rd | 76 ++--- man/Dist_Plots.Rd | 36 +- man/HD_Plots.Rd | 48 +-- man/IRF_Plots.Rd | 40 +-- src/BHSBVAR-init.c | 4 src/BHSBVAR.cpp | 527 +++++++++++++++++++++-------------------- src/RcppExports.cpp | 50 +-- vignettes/BHSBVAR.Rnw | 229 +++++++++-------- vignettes/fig/Dist_plots-1.pdf |binary vignettes/fig/HD_plots-1.pdf |binary vignettes/fig/IRF_plots-1.pdf |binary vignettes/fig/Model-1.pdf |binary 20 files changed, 908 insertions(+), 852 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt'. Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 0.2-3 dated 2018-09-18 and 0.2-4 dated 2019-01-23
DESCRIPTION | 10 ++-- MD5 | 18 +++---- R/internal.R | 4 - R/tram.R | 4 - build/partial.rdb |binary inst/NEWS.Rd | 9 +++ inst/doc/tram.pdf |binary man/tram.Rd | 4 + tests/Coxph-Ex.R | 24 ++++------ tests/Coxph-Ex.Rout.save | 106 +++++++++-------------------------------------- 10 files changed, 63 insertions(+), 116 deletions(-)
Title: Homomorphic Computations in R
Description: Homomorphic computations in R for privacy-preserving applications. Currently only
the Paillier Scheme is implemented.
Author: Balasubramanian Narasimhan [aut, cre]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between homomorpheR versions 0.2-1 dated 2017-04-28 and 0.2-2 dated 2019-01-23
DESCRIPTION | 10 +-- MD5 | 22 ++++---- build/vignette.rds |binary inst/doc/DHCox.R | 9 +-- inst/doc/DHCox.Rmd | 11 +--- inst/doc/DHCox.html | 119 +++++++++++++++++++++++++++++++++++---------- inst/doc/homomorphing.html | 88 +++++++++++++++++++++++++++++---- inst/doc/introduction.R | 1 inst/doc/introduction.Rmd | 1 inst/doc/introduction.html | 91 ++++++++++++++++++++++++++++++---- vignettes/DHCox.Rmd | 11 +--- vignettes/introduction.Rmd | 1 12 files changed, 284 insertions(+), 80 deletions(-)
Title: Spatial Visualization with ggplot2
Description: A collection of functions to visualize spatial data and models
on top of static maps from various online sources (e.g Google Maps and Stamen
Maps). It includes tools common to those tasks, including functions for
geolocation and routing.
Author: David Kahle [aut, cre],
Hadley Wickham [aut]
Maintainer: ORPHANED
Diff between ggmap versions 2.6.1 dated 2016-01-22 and 2.6.2 dated 2019-01-23
DESCRIPTION | 13 +++++++++---- MD5 | 16 ++++++++-------- inst/CITATION | 4 ++-- man/OSM_scale_lookup.Rd | 4 ++-- man/get_map.Rd | 2 ++ man/get_navermap.Rd | 4 ++-- man/get_stamenmap.Rd | 4 ++-- man/print.ggmap.Rd | 4 ++-- man/theme_nothing.Rd | 3 ++- 9 files changed, 31 insertions(+), 23 deletions(-)
Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
Author: Robert McCulloch [aut],
Rodney Sparapani [aut, cre],
Robert Gramacy [aut],
Charles Spanbauer [aut],
Matthew Pratola [aut]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between BART versions 2.1 dated 2018-11-30 and 2.2 dated 2019-01-23
BART-2.1/BART/data/Alligator.RData |only BART-2.1/BART/man/Alligator.Rd |only BART-2.2/BART/DESCRIPTION | 18 -- BART-2.2/BART/MD5 | 144 ++++++++-------- BART-2.2/BART/NAMESPACE | 11 - BART-2.2/BART/NEWS | 19 +- BART-2.2/BART/R/mbart2.R |only BART-2.2/BART/R/mc.gbart.R | 3 BART-2.2/BART/R/mc.mbart2.R |only BART-2.2/BART/R/predict.mbart.R | 2 BART-2.2/BART/R/predict.mbart2.R |only BART-2.2/BART/R/rtgamma.R |only BART-2.2/BART/R/stratrs.R | 2 BART-2.2/BART/build/vignette.rds |binary BART-2.2/BART/cleanup | 3 BART-2.2/BART/cleanup.win | 3 BART-2.2/BART/data/ACTG175.rda |binary BART-2.2/BART/data/alligator.rda |only BART-2.2/BART/data/arq.rda |binary BART-2.2/BART/data/bladder.rda |binary BART-2.2/BART/data/datalist | 2 BART-2.2/BART/data/lung.rda |binary BART-2.2/BART/data/transplant.rda |binary BART-2.2/BART/data/xdm20.test.rda |binary BART-2.2/BART/data/xdm20.train.rda |binary BART-2.2/BART/data/ydm20.test.rda |binary BART-2.2/BART/data/ydm20.train.rda |binary BART-2.2/BART/demo/00Index | 7 BART-2.2/BART/demo/alligator.R | 31 +-- BART-2.2/BART/demo/bladder.recur.bart.R | 17 + BART-2.2/BART/demo/boston.R |only BART-2.2/BART/demo/cube.gbmm.R |only BART-2.2/BART/demo/gator.mbart2.R |only BART-2.2/BART/demo/geweke.pbart2.R | 18 +- BART-2.2/BART/demo/liver.crisk.bart.R | 73 ++++---- BART-2.2/BART/demo/lung.surv.bart.R | 18 +- BART-2.2/BART/demo/nhanes.pbart1.R | 54 +++--- BART-2.2/BART/demo/nhanes.pbart2.R | 54 +++--- BART-2.2/BART/demo/replication.R |only BART-2.2/BART/demo/sparse.pbart.R | 9 - BART-2.2/BART/demo/test.rtgamma.R |only BART-2.2/BART/inst/cxx-ex/bartfuns.cpp | 2 BART-2.2/BART/inst/cxx-ex/rn.h | 17 + BART-2.2/BART/inst/doc/bincat.pdf |binary BART-2.2/BART/inst/doc/computing.pdf |binary BART-2.2/BART/inst/doc/cont1.pdf |binary BART-2.2/BART/inst/doc/cont2.pdf |binary BART-2.2/BART/inst/doc/hwbart.pdf |binary BART-2.2/BART/inst/doc/time-to-event.pdf |binary BART-2.2/BART/man/alligator.Rd |only BART-2.2/BART/man/mbart.Rd | 53 +++-- BART-2.2/BART/man/mbart2.Rd |only BART-2.2/BART/man/predict.mbart.Rd | 8 BART-2.2/BART/man/rtgamma.Rd |only BART-2.2/BART/man/rtnorm.Rd | 6 BART-2.2/BART/man/stratrs.Rd | 2 BART-2.2/BART/man/transplant.Rd | 4 BART-2.2/BART/src/bartfuns.cpp | 2 BART-2.2/BART/src/init.c | 8 BART-2.2/BART/src/rn.h | 17 + BART-2.2/BART/src/rtgamma.cpp |only BART-2.2/BART/src/rtgamma.h |only BART-2.2/BART/vignettes/figures/RI-B6-Pl.pdf |binary BART-2.2/BART/vignettes/figures/RI-Th-B6.pdf |binary BART-2.2/BART/vignettes/figures/RI-Th-Pl.pdf |binary BART-2.2/BART/vignettes/figures/alligator.pdf |binary BART-2.2/BART/vignettes/figures/boston1.pdf |binary BART-2.2/BART/vignettes/figures/boston2.pdf |binary BART-2.2/BART/vignettes/figures/boston3.pdf |binary BART-2.2/BART/vignettes/figures/boston4.pdf |binary BART-2.2/BART/vignettes/figures/boston5.pdf |binary BART-2.2/BART/vignettes/figures/boston6.pdf |binary BART-2.2/BART/vignettes/figures/clbp.pdf |binary BART-2.2/BART/vignettes/figures/geweke-pbart2-100.pdf |binary BART-2.2/BART/vignettes/figures/geweke-pbart2-1000.pdf |binary BART-2.2/BART/vignettes/figures/geweke-pbart2-10000.pdf |binary BART-2.2/BART/vignettes/figures/geweke-pbart2-200.pdf |only BART-2.2/BART/vignettes/figures/liver-BART.pdf |binary BART-2.2/BART/vignettes/figures/lung.pdf |binary BART-2.2/BART/vignettes/figures/neck.pdf |binary BART-2.2/BART/vignettes/figures/sparse-pbart.pdf |binary BART-2.2/BART/vignettes/references.bib | 85 ++++----- 82 files changed, 405 insertions(+), 287 deletions(-)
Title: 'NatureServe' Interface
Description: Interface to 'NatureServe' (<http://www.natureserve.org>).
Includes methods to get data, image metadata, search taxonomic names,
and make maps.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between natserv versions 0.1.4 dated 2017-01-03 and 0.3.0 dated 2019-01-23
DESCRIPTION | 32 +++++++++------- LICENSE | 2 - MD5 | 49 ++++++++++++++++--------- NEWS.md | 20 ++++++++++ R/http.R | 27 +++++++++++++- R/ns_data.R | 14 ++++++- R/ns_images.R | 15 ++++++- R/ns_search.R | 2 + R/zzz.R | 30 ++++++++++++++- README.md | 63 +++++++++++++++++---------------- build |only inst |only man/nat_states.Rd | 1 man/natserv-package.Rd | 3 - man/ns_data.Rd | 7 ++- man/ns_images.Rd | 4 +- man/ns_map.Rd | 3 - man/ns_search.Rd | 4 +- tests/fixtures |only tests/testthat/helper-natserv.R |only tests/testthat/test-internal_tooling.R |only tests/testthat/test-ns_data.R | 33 ++++++++++++++++- tests/testthat/test-ns_images.R | 28 ++++++++++++++ tests/testthat/test-ns_search.R | 19 +++++++++ vignettes |only 25 files changed, 274 insertions(+), 82 deletions(-)
Title: Visualize Genomic Mutation Data Using an Interactive Lollipop
Diagram
Description: R interface for 'g3viz' JavaScript library. Using an interactive lollipop diagram to visualize genomic mutation data in a web browser.
Author: Xin Guo [aut, cre]
Maintainer: Xin Guo <phoeguo@gmail.com>
Diff between g3viz versions 0.1.3 dated 2018-08-30 and 0.1.4 dated 2019-01-23
g3viz-0.1.3/g3viz/inst/extdata/CCLE_APC.png |only g3viz-0.1.3/g3viz/inst/extdata/MSK_IMPACT_2017_TP53.png |only g3viz-0.1.3/g3viz/inst/extdata/TCGA_BRCA_PIK3CA.png |only g3viz-0.1.4/g3viz/DESCRIPTION | 16 ++++++++++------ g3viz-0.1.4/g3viz/MD5 | 15 ++++++++++----- g3viz-0.1.4/g3viz/R/hgnc2pfam.R | 2 ++ g3viz-0.1.4/g3viz/build |only g3viz-0.1.4/g3viz/inst/doc |only g3viz-0.1.4/g3viz/vignettes |only 9 files changed, 22 insertions(+), 11 deletions(-)
Title: Fast Covariance Estimation for Sparse Functional Data
Description: We implement the Fast Covariance Estimation for Sparse Functional Data paper published in Statistics and Computing <doi: 10.1007/s11222-017-9744-8>.
Author: Luo Xiao [aut,cre], Cai Li [aut], William Checkley [aut], Ciprian
Crainiceanu [aut]
Maintainer: Luo Xiao <lxiao5@ncsu.edu>
Diff between face versions 0.1-4 dated 2018-01-19 and 0.1-5 dated 2019-01-23
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- R/face.sparse.inner.r | 23 ++++++++++++++++------- build/partial.rdb |binary man/face-package.Rd | 4 ++-- man/pspline.Rd | 2 ++ 6 files changed, 31 insertions(+), 20 deletions(-)
Title: Search and Retrieve Scientific Publication Records from PubMed
Description: Query NCBI Entrez and retrieve PubMed records in XML or text format. Process PubMed records by extracting and aggregating data from selected fields. A large number of records can be easily downloaded via this simple-to-use interface to the NCBI PubMed API.
Author: Damiano Fantini
Maintainer: Damiano Fantini <damiano.fantini@gmail.com>
Diff between easyPubMed versions 2.5 dated 2018-05-06 and 2.11 dated 2019-01-23
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Title: Continuous-Time Fractionally Integrated ARMA Process for
Irregularly Spaced Long-Memory Time Series Data
Description: We provide a toolbox to fit a continuous-time fractionally integrated ARMA process (CARFIMA) on univariate and irregularly spaced time series data via frequentist or Bayesian machinery. A general-order CARFIMA(p, H, q) model for p>q is specified in Tsai and Chan (2005) <doi:10.1111/j.1467-9868.2005.00522.x> and it involves (p+q+2) unknown model parameters, i.e., p AR parameters, q MA parameters, Hurst parameter H, and process uncertainty (standard deviation) sigma. The package produces their maximum likelihood estimates and asymptotic uncertainties using a global optimizer called the differential evolution algorithm. It also produces their posterior distributions via Metropolis within a Gibbs sampler equipped with adaptive Markov chain Monte Carlo for posterior sampling. These fitting procedures, however, may produce numerical errors if p>2. The toolbox also contains a function to simulate discrete time series data from CARFIMA(p, H, q) process given the model parameters and observation times.
Author: Hyungsuk Tak [aut] (<https://orcid.org/0000-0003-0334-8742>),
Henghsiu Tsai [aut],
Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyou@nd.edu>
Diff between carfima versions 2.0.0 dated 2018-11-01 and 2.0.1 dated 2019-01-23
DESCRIPTION | 11 MD5 | 26 NAMESPACE | 5 NEWS.md |only R/RcppExports.R | 8 R/carfima.R | 1467 ++++++++++++++++++------------------- R/carfima.loglik.R | 90 +- R/noRD.carfima.loglik.nosigma.R | 2 R/package-carfima.R | 4 README.md |only build/partial.rdb |binary src/RcppExports.cpp | 16 src/auxiliary.cpp | 33 src/cpp_carfima_loglik.cpp | 2 src/cpp_carfima_loglik_nosigma.cpp | 12 15 files changed, 831 insertions(+), 845 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-27 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-26 0.2.0
2017-10-23 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-01 2.4.2
2016-09-21 2.4.0
2014-01-02 2.3
2012-01-13 2.0
2010-11-08 1.9
2010-10-19 1.8
2010-10-04 1.7
2009-10-18 1.6.4
2009-04-26 1.6
2009-01-13 1.5
2009-01-12 1.4
2008-11-25 1.2
2008-11-21 1.1
2008-09-09 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-15 0.1.0